Menopause is characterized by the cessation of menstruation and a decline in reproductive function,which is an intrinsic component of the aging process.However,it has been a frequently overlooked field of women’s hea...Menopause is characterized by the cessation of menstruation and a decline in reproductive function,which is an intrinsic component of the aging process.However,it has been a frequently overlooked field of women’s health.The oral and gut microbiota,constituting the largest ecosystem within the human body,are important for maintaining human health and notably contribute to the healthy aging of menopausal women.Therefore,a comprehensive review elucidating the impact of the gut and oral microbiota on menopause for healthy aging is of paramount importance.This paper presents the current understanding of the microbiome during menopause,with a particular focus on alterations in the oral and gut microbiota.Our study elucidates the complex interplay between the microbiome and sex hormone levels,explores microbial crosstalk dynamics,and investigates the associations between the microbiome and diseases linked to menopause.Additionally,this review explores the potential of microbiome-targeting therapies for managing menopause-related diseases.Given that menopause can last for approximately 30 years,gaining insights into how the microbiome and menopause interact could pave the way for innovative interventions,which may result in symptomatic relief from menopause and an increase in quality of life in women.展开更多
BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut mic...BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut microbiome.There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis.AIM To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA patients.METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA.Analytical techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway analysis.RESULTS Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(S.gallolyticus),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA patients.Mediterraneibacter gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA groups.Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);S.gallolyticus was a major contributor.Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,whereas TA patients exhibited co-occurrence of CRC-associated bacteria.Furthermore,the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients.CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development,providing insights concerning the roles of microbial species,functional pathways,and microbial interactions in colorectal carcinogenesis.展开更多
Biodiversity has become a terminology familiar to virtually every citizen in modern societies.It is said that ecology studies the economy of nature,and economy studies the ecology of humans;then measuring biodiversity...Biodiversity has become a terminology familiar to virtually every citizen in modern societies.It is said that ecology studies the economy of nature,and economy studies the ecology of humans;then measuring biodiversity should be similar with measuring national wealth.Indeed,there have been many parallels between ecology and economics,actually beyond analogies.For example,arguably the second most widely used biodiversity metric,Simpson(1949)’s diversity index,is a function of familiar Gini-index in economics.One of the biggest challenges has been the high“diversity”of diversity indexes due to their excessive“speciation”-there are so many indexes,similar to each country’s sovereign currency-leaving confused diversity practitioners in dilemma.In 1973,Hill introduced the concept of“numbers equivalent”,which is based on Renyi entropy and originated in economics,but possibly due to his abstruse interpretation of the concept,his message was not widely received by ecologists until nearly four decades later.What Hill suggested was similar to link the US dollar to gold at the rate of$35 per ounce under the Bretton Woods system.The Hill numbers now are considered most appropriate biodiversity metrics system,unifying Shannon,Simpson and other diversity indexes.Here,we approach to another paradigmatic shift-measuring biodiversity on ecological networks-demonstrated with animal gastrointestinal microbiomes representing four major invertebrate classes and all six vertebrate classes.The network diversity can reveal the diversity of species interactions,which is a necessary step for understanding the spatial and temporal structures and dynamics of biodiversity across environmental gradients.展开更多
Background Nursery pigs undergo stressors in the post-weaning period that result in production and welfare chal-lenges.These challenges disproportionately impact the offspring of primiparous sows compared to those of ...Background Nursery pigs undergo stressors in the post-weaning period that result in production and welfare chal-lenges.These challenges disproportionately impact the offspring of primiparous sows compared to those of mul-tiparous counterparts.Little is known regarding potential interactions between parity and feed additives in the post-weaning period and their effects on nursery pig microbiomes.Therefore,the objective of this study was to investigate the effects of maternal parity on sow and offspring microbiomes and the influence of sow parity on pig fecal microbi-ome and performance in response to a prebiotic post-weaning.At weaning,piglets were allotted into three treat-ment groups:a standard nursery diet including pharmacological doses of Zn and Cu(Con),a group fed a commercial prebiotic only(Preb)based on an Aspergillus oryzae fermentation extract,and a group fed the same prebiotic plus Zn and Cu(Preb+ZnCu).Results Although there were no differences in vaginal microbiome composition between primiparous and mul-tiparous sows,fecal microbiome composition was different(R^(2)=0.02,P=0.03).The fecal microbiomes of primiparous offspring displayed significantly higher bacterial diversity compared to multiparous offspring at d 0 and d 21 post-weaning(P<0.01),with differences in community composition observed at d 21(R^(2)=0.03,P=0.04).When analyzing the effects of maternal parity within each treatment,only the Preb diet triggered significant microbiome distinc-tions between primiparous and multiparous offspring(d 21:R^(2)=0.13,P=0.01;d 42:R^(2)=0.19,P=0.001).Composi-tional differences in pig fecal microbiomes between treatments were observed only at d 21(R^(2)=0.12,P=0.001).Pigs in the Con group gained significantly more weight throughout the nursery period when compared to those in the Preb+ZnCu group.Conclusions Nursery pig gut microbiome composition was influenced by supplementation with an Aspergillus oryzae fermentation extract,with varying effects on performance when combined with pharmacological levels of Zn and Cu or for offspring of different maternal parity groups.These results indicate that the development of nursery pig gut microbiomes is shaped by maternal parity and potential interactions with the effects of dietary feed additives.展开更多
Monitoring the prevalence of antimicrobial resistance genes(ARGs)is vital for addressing the global crisis of antibiotic-resistant bacterial infections.Despite its importance,the characterization of ARGs and microbiom...Monitoring the prevalence of antimicrobial resistance genes(ARGs)is vital for addressing the global crisis of antibiotic-resistant bacterial infections.Despite its importance,the characterization of ARGs and microbiome structures,as well as the identification of indicators for routine ARG monitoring in pig farms,are still lacking,particularly concerning variations in antimicrobial exposure in different countries or regions.Here,metagenomics and random forest machine learning were used to elucidate the ARG profiles,microbiome structures,and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe.Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs(P<0.05).ANT(6)-Ib,APH(3')-IIIa,and tet(40)were identified as shared core ARGs between the two pig populations.Furthermore,the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions.Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs,respectively.Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100%and 98.7%,respectively.Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy(r=0.72-0.88).Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs.The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.展开更多
The "Biofilms, Microbiomes and Oral Diseases: Challenges and Future Perspectives" symposium jointly organized by Penn Dental Medicine and West China School of Stomatology was held on 30 September 2017 at Pen...The "Biofilms, Microbiomes and Oral Diseases: Challenges and Future Perspectives" symposium jointly organized by Penn Dental Medicine and West China School of Stomatology was held on 30 September 2017 at Penn Wharton China Center(PWCC) in Beijing,China. The topics included the pathogenicity of oral biofilms, novel strategies for the control of biofilm-related diseases, oral microbiome and single-cell approaches, and the link between oral diseases and overall health. Researchers from a number of disciplines, representing institutions from China and Penn Dental Medicine, gathered to discuss advances in our understanding of biofilms, as well as future directions for the control of biofilm-related oral and systemic diseases.展开更多
Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with dr...Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.展开更多
Children are less susceptible to coronavirus disease 2019 (COVID-19), and they have manifested lower morbidity and mortality after infection, for which a multitude of mechanisms may be considered. Whether the normal d...Children are less susceptible to coronavirus disease 2019 (COVID-19), and they have manifested lower morbidity and mortality after infection, for which a multitude of mechanisms may be considered. Whether the normal development of the gut-airway microbiome in children is affected by COVID-19 has not been evaluated. Here, we demonstrate that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)infection alters the upper respiratory tract and the gut microbiomes in nine children. The alteration of the microbiome is dominated by the genus Pseudomonas, and it sustains for up to 25e58 days in different individuals. Moreover, the patterns of alternation are different between the upper respiratory tract and the gut. Longitudinal investigation shows that the upper respiratory tract and the gut microbiomes are extremely variable among children during the course of COVID-19. The dysbiosis of microbiome persists in7 of 8 children for at least 19e24 days after discharge from the hospital. Disturbed development of both the gut and the upper respiratory microbiomes and prolonged dysbiosis in these nine children imply possible long-term complications after clinical recovery from COVID-19, such as predisposition to the increased health risk in the post-COVID-19 era.展开更多
Background:The greatest impact on profitability of a commercial beef operation is reproduction.However,in beef heifers,little is known about the vaginal and fecal microbiota with respect to their relationship with fer...Background:The greatest impact on profitability of a commercial beef operation is reproduction.However,in beef heifers,little is known about the vaginal and fecal microbiota with respect to their relationship with fertility.To this end,we followed heifers through gestation to examine the dynamics of vaginal and fecal microbial composition throughout pregnancy.Results:Heifers were exposed to an estrus synchronization protocol,observed over a 12-day period,artificially inseminated 12 h to 18 h after observed estrus,and subsequently exposed to bulls for a 50-day breeding season.Vaginal samples were taken at pre-breeding(n=72),during the first(n=72),and second trimester(n=72)for all individuals,and third trimester for individuals with confirmed pregnancies(n=56).Fecal samples were taken at prebreeding(n=32)and during the first trimester(n=32),including bred and open individuals.Next generation sequencing of the V4 region of the 16 S rRNA gene via the Illumina Mi Seq platform was applied to all samples.Shannon indices and the number of observed bacterial features were the same in fecal samples.However,significant differences in vaginal microbiome diversity between gestation stages were observed.No differences in beta-diversity were detected in vaginal or fecal samples regarding pregnancy status,but such differences were seen with fecal microbiome over time.Random Forest was developed to identify predictors of pregnancy status in vaginal(e.g.,Histophilus,Clostridiaceae,Campylobacter)and fecal(e.g.,Bacteroidales,Dorea)samples.Conclusions:Our study shows that bovine vaginal and fecal microbiome could be used as biomarkers of bovine reproduction.Further experiments are needed to validate these biomarkers and to examine their roles in a female’s ability to establish pregnancy.展开更多
One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being ele...One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being elevation of inorganic phosphate concentrations around feces depositions.The complex soil biochemistry in the region makes it difficult to define the causal factors of these changes using common research approaches.Here,we addressed the effects of phosphate alone on microbiome structure and dynamics over time by adding external phosphate to selected soils in the Antarctic region.We then analyzed the soil bacterial community composition and diversity using 16S rRNA amplicon sequencing and compared these data with phosphate levels.Parallel geochemical analysis revealed changes in nine soil geochemical factors upon phosphate addition,all of which were relevant to microbiome structure,with soil pH showing the highest correlation.Links between geochemical factors and composition were identified,as were interactions between bacterial taxa.Additionally,Sphingobacteriia,Sphingobacteriales and Chitinophagaceae were found to be more abundant in phosphate-treated soils.Co-occurrence network analysis revealed significantly increased levels of associations in all major network properties over time after phosphate supplementation.Therefore,we conclude phosphate addition has diverse effects on Antarctic soil microbiomes.展开更多
Microorganisms are integral inhabitants of plants,playing a crucial role in plant growth,development,and health.The composition and diversity of microorganisms in plants can be influenced by several factors,including ...Microorganisms are integral inhabitants of plants,playing a crucial role in plant growth,development,and health.The composition and diversity of microorganisms in plants can be influenced by several factors,including environmental factors such as soil type,temperature,and water availability.The plant microbiome serves essential functions,including nutrient acquisition,disease resistance,and stress tolerance,achieved through complex interactions between microorganisms and plants.Understanding these interactions and the impact of environmental factors can provide valuable insights into developing sustainable agricultural practices.The use of plant microbiomes in agriculture has the potential to improve crop yield,reduce fertilizer and pesticide use,and enhance soil health and sustainability,but scaling up these technologies poses several challenges.The potential benefits of using plant microbiomes in agriculture are significant and could revolutionize the industry.However,scaling up these technologies presents several challenges that require further research and innovation.In conclusion,studying plant microbiomes has the potential to bring about positive impacts for farmers,consumers,and the environment.展开更多
Macroalgae farming not only holds significant economic value but also contributes substantially to carbon sequestration,and therefore has gained intensified attention globally under climate change scenarios.However,it...Macroalgae farming not only holds significant economic value but also contributes substantially to carbon sequestration,and therefore has gained intensified attention globally under climate change scenarios.However,its sustainability is increasingly threatened by anthropogenic and environmental changes.The health and resilience of macroalgae are intrinsically linked to their associated microbiomes,offering an untapped opportunity to enhance macroalgal farming through microbiome manipulation.In this review,we have summarized the current understanding of macroalgal microbiomes,highlighting critically underexplored microbial components,such as overlooked taxa,host specificity,and the environmental factors influencing microbiome composition,which hinder the development of effective microbiome engineering strategies.We critically evaluate existing microbiome manipulation approaches and their applications in enhancing macroalgal growth,resilience,carbon fixation,and biomass yield and assess their potential for improving macroalgal carbon sequestration.Finally,we propose a holistic framework that integrates multi-omics and metabolic modeling,microbial functional and environmental compatibility,high-throughput rapid isolation,and in vivo validation to bridge critical knowledge gaps and unlock the full potential of macroalgal microbiome engineering for sustainable,large-scale macroalgal farming.展开更多
Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome,the gut morphology is seldom independently considered and even often ignored.To address this research gap,we investigated a ...Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome,the gut morphology is seldom independently considered and even often ignored.To address this research gap,we investigated a large-scale dataset of mammalian gut microbiomes,comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders.We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories(foregut/hindgut/simple,foregut/hindgut,functional ruminant/ruminant-like,and colon fermenter/cecum fermenter)and uncovered the synergistic effect between phylogeny and gut morphology.Moreover,we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches,as well as those within the same taxonomic order but with different gut morphologies.We also identified three enterotype indices—Fusobacterium,UCG-005,and Prevotella—which could predict the three gut morphology types of mammals:simple,foregut,and hindgut.These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.展开更多
Microbes play a crucial ecological role in soils,but the presence of relic DNA left by previous microorganisms can lead to inaccurate estimations of viable microbial function and diversity.To address this,we proposed ...Microbes play a crucial ecological role in soils,but the presence of relic DNA left by previous microorganisms can lead to inaccurate estimations of viable microbial function and diversity.To address this,we proposed a new method for removing relic DNA in soil using Benzonase endonuclease and compared it with propidium monoazide(PMA)and DNase I,which have been widely applied in viable microbiome studies.Unlike PMA,Benzonase does not require light activation and is suitable for use in opaque media such as soil.Therefore,its efficiency(40%-60%)in removing soil relic DNA was twice that of PMA(0-30%).Moreover,our results showed that Benzonase outperformed DNase I in most soils,probably due to its broader range of operating conditions compared to DNase I.In addition to higher relic DNA removal efficiency,Benzonase exhibited a weak impact on soil viable microbial communities.Subsequently,Benzonase was used to remove relic DNA in natural soils,and the results showed that relic DNA removal led to an approximately 10%reduction in microbial diversity and richness on average.Notably,it caused significant changes in the relative abundance of specific taxa,such as Bacillus and Sphingomonas.These findings reveal disparities between total and viable microbiomes in soils.Our study not only provides a reliable method for soil relic DNA removal but also highlights the necessity of relic DNA removal for viable soil microbiome assessments,laying the methodological foundation for advancing soil microbial ecology research.展开更多
Soils are not exempt from anthropogenic pollution,which can eventually cause disturbance of the microbial communities and areas without any kind of productivity.Among soil microbiota,bacteria play an important role in...Soils are not exempt from anthropogenic pollution,which can eventually cause disturbance of the microbial communities and areas without any kind of productivity.Among soil microbiota,bacteria play an important role in pollutant degradation,enabling them to thrive in contaminated sites.Given this,several techniques have been used to increase the number of pollutantdegrading bacteria in situ or for subsequent addition.Additionally,bacteriophages exhibit a high tolerance to pollutants and enhance bacterial metabolic activity through phage-encoded auxiliary metabolic genes(AMGs),thereby augmenting their skills for nutrient assimilation,resistance to phage infection,antibiotic resistance,heavy metal resistance,and degradation of pesticides and xenobiotics,among others.Several phage-encoded AMGs have been described during the last few years,but their diversity,distribution,and function have not been extensively explored,warranting further studies.Here,we highlight soil microbiome interactions,especially bacterium and phage interactions to understand this unexplored world with a high potential for restoring polluted soils.展开更多
Regulating electron transfer in predominantly fermentative microbiomes has broad implications in environmental,chemical,food,and medical fields.Here we demonstrate electrochemical control in fermenting food waste,dige...Regulating electron transfer in predominantly fermentative microbiomes has broad implications in environmental,chemical,food,and medical fields.Here we demonstrate electrochemical control in fermenting food waste,digestate,and wastewater to improve lactic acid production.We hypothesize that applying anodic potential will expedite and direct fermentation towards lactic acid.Continued operation that introduced epi/endophytic communities(Lactococcus,Lactobacillus,Weissella)to pure culture Lactiplantibacillus plantarum reactors with static electrodes was associated with the loss of anode-induced process intensification despite 80%L.plantarum retention.Employing fluidized electrodes discouraged biofilm formation and extended electrode influence to planktonic gram-positive fermenters using mediated extracellular electron transfer.While short-term experiments differentially enriched Lactococcus and Klebsiella spp.,longer-term operations indicated convergent microbiomes and product spectra.These results highlight a functional resilience of environmental fermentative microbiomes to perturbations in redox potential,underscoring the need to better understand electrode induced polymicrobial interactions and physiological impacts to engineer tunable open-culture or synthetic consortia.展开更多
Despite the growing awareness on the importance of gut microbiomes,understanding marine mammal gut microbiomes remains limited due to difficulties in sampling.Spotted dolphins(Stenella attenuata)are widely spread ocea...Despite the growing awareness on the importance of gut microbiomes,understanding marine mammal gut microbiomes remains limited due to difficulties in sampling.Spotted dolphins(Stenella attenuata)are widely spread oceanic cetaceans,and there is a gap in knowledge regarding their gut microbiology.In this study,we opportunistically collected samples from both wild and human-cared spotted dolphins in the southern waters of Hainan Island,China.This provided the opportunity to examine the composition and diversity of the gut microbial communities of this cetacean species.Since these dolphins inhabit a similar water environment,different food sources might be the primary factor distinguishing the gut microbiomes of wild and human-cared populations,offering valuable experimental material to investigate potential differences in gut microbial community structure among marine mammals in similar environments but with varying food sources.We found that the gastrointestinal microbial community structure of wild and human-cared dolphins demonstrated significant differences,both overall and at specific locations.However,no significant difference was observed in the microbial diversity of their gastrointestinal tracts,indicating that the disparities primarily lie in microbiota composition.Additionally,we detected numerous potentially pathogenic bacteria,suggesting a comprehensive future study of marine mammal gut microbiology.Such a study might involve determining health indicator factors associated with these microbiomes.Our study not only supplements information on the gut microbiology of spotted dolphins but also delves into the similarities and differences in gastrointestinal microbial communities within the same marine mammal species when food source variations play a significant role in their lives.展开更多
BACKGROUND Autoimmune liver diseases,including primary biliary cholangitis(PBC),autoi-mmune hepatitis(AIH),and their overlap syndrome(OS),involve immune-mediated liver injury,with OS occurring in 1.2%-25%of PBC patien...BACKGROUND Autoimmune liver diseases,including primary biliary cholangitis(PBC),autoi-mmune hepatitis(AIH),and their overlap syndrome(OS),involve immune-mediated liver injury,with OS occurring in 1.2%-25%of PBC patients.OS carries a higher risk of cirrhosis,hepatocellular carcinoma,and reduced survival.While its pathogenesis remains unclear,gut microbiota dysbiosis and serum metabolite alterations may play key roles.This study uses 16S rRNA sequencing and liquid chromatography-mass spec-trometry(LC-MS)metabolomics to compare gut microbiota and serum metabolites among PBC,AIH,and OS patients,and explores their associations with liver function.AIM To differentiate OS from PBC and AIH based on gut microbiota,serum metabolites,and liver function.METHODS Gut microbiota profiles were analyzed using 16S rRNA sequencing,while untargeted serum metabolomics was conducted via LC-MS.Comparative analyses were performed to identify differences in microbial composition and serum metabolite levels among PBC,AIH,and OS groups.Correlation analyses and network visualization tech-niques were applied to elucidate the interactions among liver function parameters,gut microbiota,and serum metabolites in OS patients.RESULTS Compared to patients with PBC or AIH,OS patients demonstrated significantly reduced microbial diversity and richness.Notable taxonomic shifts included decreased abundances of Firmicutes,Bacteroidetes,and Actinobacteria,alongside increased levels of Proteobacteria and Verrucomicrobia.Distinct serum metabolites,such as pentadecanoic acid and aminoimidazole carboxamide ribonucleotide,were identified in OS patients.Correlation analysis revealed that aspartate aminotransferase(AST)levels were negatively associated with the bacterial genus Fusicatenibacter and the metabolite L-Tyrosine.A microbial-metabolite network diagram further confirmed a strong association between Fusicatenibacter and L-Tyrosine in OS patients.CONCLUSION OS patients show decreased gut microbiota diversity and unique serum metabolites.Multi-omics linked AST,Fusicatenibacter,and L-Tyrosine,revealing OS mechanisms and diagnostic potential.展开更多
BACKGROUND Hepatic fibrosis(HF)represents a pivotal stage in the progression and potential reversal of cirrhosis,underscoring the importance of early identification and therapeutic intervention to modulate disease tra...BACKGROUND Hepatic fibrosis(HF)represents a pivotal stage in the progression and potential reversal of cirrhosis,underscoring the importance of early identification and therapeutic intervention to modulate disease trajectory.AIM To explore the complex relationship between chronic hepatitis B(CHB)-related HF and gut microbiota to identify microbiota signatures significantly associated with HF progression in CHB patients using advanced machine learning algorithms.METHODS This study included patients diagnosed with CHB and classified them into HF and non-HF groups based on liver stiffness measurements.The HF group was further subdivided into four subgroups:F1,F2,F3,and F4.Data on clinical indicators were collected.Stool samples were collected for 16S rRNA sequencing to assess the gut microbiome.Microbiota diversity,relative abundance,and linear discriminant analysis effect size(LEfSe)were analyzed in different groups.Correlation analysis between clinical indicators and the relative abundance of gut microbiota was performed.The random forest and eXtreme gradient boosting algorithms were used to identify key differential gut microbiota.The Shapley additive explanations were used to evaluate microbiota importance.RESULTS Integrating the results from univariate analysis,LEfSe,and machine learning,we identified that the presence of Dorea in gut microbiota may be a key feature associated with CHB-related HF.Dorea possibly serves as a core differential feature of the gut microbiota that distinguishes HF from non-HF patients,and the presence of Dorea shows significant variations across different stages of HF(P<0.05).The relative abundance of Dorea significantly decreases with increasing HF severity(P=0.041).Moreover,the gut microbiota composition in patients with different stages of HF was found to correlate with several liver function indicators,such asγ-glutamyl transferase,alkaline phosphatase,total bilirubin,and the aspartate aminotransferase/alanine transaminase ratio(P<0.05).The associated pathways were predominantly enriched in biosynthesis,degradation/utilization/assimilation,generation of precursors,metabolites,and energy,among other categories.CONCLUSION HF affects the composition of the gut microbiota,indicating that the gut microbiota plays a crucial role in its pathophysiological processes.The abundance of Dorea varies significantly across various stages of HF,making it a potential microbial marker for identifying HF onset and progression.展开更多
Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms hel...Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms help human body against invasion of undesirable stim- ulation outside. However, imbalance of microbial flora contributes to oral diseases and systemic diseases. Oral microbiomes play an important role in the human microbial community and human health. The use of recently developed molecular methods has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Studies in oral microbiomes and their interactions with microbiomes in variable body sites and variable health condition are critical in our cognition of our body and how to make effect on human health improvement.展开更多
基金supported by Science&Technology Fundamental Resources Investigation Program(2022FY100800)the CAMS Innovation Fund for Medical Sciences(CIFMS)(2021-12M-1-023/2023-12M-C&T-B-005)+1 种基金Funding for Reform and Development of Beijing Municipal Health Commissionthe National High Level Hospital Clinical Research Funding(2022-PUMCH-B-094).
文摘Menopause is characterized by the cessation of menstruation and a decline in reproductive function,which is an intrinsic component of the aging process.However,it has been a frequently overlooked field of women’s health.The oral and gut microbiota,constituting the largest ecosystem within the human body,are important for maintaining human health and notably contribute to the healthy aging of menopausal women.Therefore,a comprehensive review elucidating the impact of the gut and oral microbiota on menopause for healthy aging is of paramount importance.This paper presents the current understanding of the microbiome during menopause,with a particular focus on alterations in the oral and gut microbiota.Our study elucidates the complex interplay between the microbiome and sex hormone levels,explores microbial crosstalk dynamics,and investigates the associations between the microbiome and diseases linked to menopause.Additionally,this review explores the potential of microbiome-targeting therapies for managing menopause-related diseases.Given that menopause can last for approximately 30 years,gaining insights into how the microbiome and menopause interact could pave the way for innovative interventions,which may result in symptomatic relief from menopause and an increase in quality of life in women.
基金Supported by Chulabhorn Royal Academy(Fundamental Fund:Fiscal year 2022 by National Science Research and Innovation Fund),No.FRB650039/0240 Project Code 165422.
文摘BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut microbiome.There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis.AIM To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA patients.METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA.Analytical techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway analysis.RESULTS Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(S.gallolyticus),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA patients.Mediterraneibacter gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA groups.Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);S.gallolyticus was a major contributor.Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,whereas TA patients exhibited co-occurrence of CRC-associated bacteria.Furthermore,the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients.CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development,providing insights concerning the roles of microbial species,functional pathways,and microbial interactions in colorectal carcinogenesis.
基金supported by the National Natural Science Foundation of China(31970116,72274192)。
文摘Biodiversity has become a terminology familiar to virtually every citizen in modern societies.It is said that ecology studies the economy of nature,and economy studies the ecology of humans;then measuring biodiversity should be similar with measuring national wealth.Indeed,there have been many parallels between ecology and economics,actually beyond analogies.For example,arguably the second most widely used biodiversity metric,Simpson(1949)’s diversity index,is a function of familiar Gini-index in economics.One of the biggest challenges has been the high“diversity”of diversity indexes due to their excessive“speciation”-there are so many indexes,similar to each country’s sovereign currency-leaving confused diversity practitioners in dilemma.In 1973,Hill introduced the concept of“numbers equivalent”,which is based on Renyi entropy and originated in economics,but possibly due to his abstruse interpretation of the concept,his message was not widely received by ecologists until nearly four decades later.What Hill suggested was similar to link the US dollar to gold at the rate of$35 per ounce under the Bretton Woods system.The Hill numbers now are considered most appropriate biodiversity metrics system,unifying Shannon,Simpson and other diversity indexes.Here,we approach to another paradigmatic shift-measuring biodiversity on ecological networks-demonstrated with animal gastrointestinal microbiomes representing four major invertebrate classes and all six vertebrate classes.The network diversity can reveal the diversity of species interactions,which is a necessary step for understanding the spatial and temporal structures and dynamics of biodiversity across environmental gradients.
基金This study was partially supported by funds from the Agricultural Research,Education,Extension and Technology Transfer(AGREETT)and MNDrive Global Food Ventures Programs,both from the University of MinnesotaPartial funding was supplied by BioZyme,Inc,St.Joseph,Missouri,USA and New Fashion Pork,Jackson,MN,USA.
文摘Background Nursery pigs undergo stressors in the post-weaning period that result in production and welfare chal-lenges.These challenges disproportionately impact the offspring of primiparous sows compared to those of mul-tiparous counterparts.Little is known regarding potential interactions between parity and feed additives in the post-weaning period and their effects on nursery pig microbiomes.Therefore,the objective of this study was to investigate the effects of maternal parity on sow and offspring microbiomes and the influence of sow parity on pig fecal microbi-ome and performance in response to a prebiotic post-weaning.At weaning,piglets were allotted into three treat-ment groups:a standard nursery diet including pharmacological doses of Zn and Cu(Con),a group fed a commercial prebiotic only(Preb)based on an Aspergillus oryzae fermentation extract,and a group fed the same prebiotic plus Zn and Cu(Preb+ZnCu).Results Although there were no differences in vaginal microbiome composition between primiparous and mul-tiparous sows,fecal microbiome composition was different(R^(2)=0.02,P=0.03).The fecal microbiomes of primiparous offspring displayed significantly higher bacterial diversity compared to multiparous offspring at d 0 and d 21 post-weaning(P<0.01),with differences in community composition observed at d 21(R^(2)=0.03,P=0.04).When analyzing the effects of maternal parity within each treatment,only the Preb diet triggered significant microbiome distinc-tions between primiparous and multiparous offspring(d 21:R^(2)=0.13,P=0.01;d 42:R^(2)=0.19,P=0.001).Composi-tional differences in pig fecal microbiomes between treatments were observed only at d 21(R^(2)=0.12,P=0.001).Pigs in the Con group gained significantly more weight throughout the nursery period when compared to those in the Preb+ZnCu group.Conclusions Nursery pig gut microbiome composition was influenced by supplementation with an Aspergillus oryzae fermentation extract,with varying effects on performance when combined with pharmacological levels of Zn and Cu or for offspring of different maternal parity groups.These results indicate that the development of nursery pig gut microbiomes is shaped by maternal parity and potential interactions with the effects of dietary feed additives.
基金supported by the Foundation for the National Key R&D Program(2022YFD1800400)Innovative Research Groups of the National Natural Science Foundation of China(32121004)Natural Science Foundation of Guangdong Province of China(2021A1515011159)。
文摘Monitoring the prevalence of antimicrobial resistance genes(ARGs)is vital for addressing the global crisis of antibiotic-resistant bacterial infections.Despite its importance,the characterization of ARGs and microbiome structures,as well as the identification of indicators for routine ARG monitoring in pig farms,are still lacking,particularly concerning variations in antimicrobial exposure in different countries or regions.Here,metagenomics and random forest machine learning were used to elucidate the ARG profiles,microbiome structures,and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe.Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs(P<0.05).ANT(6)-Ib,APH(3')-IIIa,and tet(40)were identified as shared core ARGs between the two pig populations.Furthermore,the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions.Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs,respectively.Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100%and 98.7%,respectively.Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy(r=0.72-0.88).Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs.The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.
基金in part made possible through Penn Global Education Fund
文摘The "Biofilms, Microbiomes and Oral Diseases: Challenges and Future Perspectives" symposium jointly organized by Penn Dental Medicine and West China School of Stomatology was held on 30 September 2017 at Penn Wharton China Center(PWCC) in Beijing,China. The topics included the pathogenicity of oral biofilms, novel strategies for the control of biofilm-related diseases, oral microbiome and single-cell approaches, and the link between oral diseases and overall health. Researchers from a number of disciplines, representing institutions from China and Penn Dental Medicine, gathered to discuss advances in our understanding of biofilms, as well as future directions for the control of biofilm-related oral and systemic diseases.
文摘Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.
基金supported by the grants from the National Key Research and Development Program of China (2018YFC2000500 and 2017ZX10103009002)Major Science and Technology Project in Yunnan Province of China (202001BB050001)+3 种基金the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0503)the Key Research Program of the Chinese Academy of Sciences (FZDSW219)the Chinese National Natural Science Foundation of China (31970571)grants specific for coronavirus disease 2019 from the Children’s Hospital of Fudan University (EKXGZX006)。
文摘Children are less susceptible to coronavirus disease 2019 (COVID-19), and they have manifested lower morbidity and mortality after infection, for which a multitude of mechanisms may be considered. Whether the normal development of the gut-airway microbiome in children is affected by COVID-19 has not been evaluated. Here, we demonstrate that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)infection alters the upper respiratory tract and the gut microbiomes in nine children. The alteration of the microbiome is dominated by the genus Pseudomonas, and it sustains for up to 25e58 days in different individuals. Moreover, the patterns of alternation are different between the upper respiratory tract and the gut. Longitudinal investigation shows that the upper respiratory tract and the gut microbiomes are extremely variable among children during the course of COVID-19. The dysbiosis of microbiome persists in7 of 8 children for at least 19e24 days after discharge from the hospital. Disturbed development of both the gut and the upper respiratory microbiomes and prolonged dysbiosis in these nine children imply possible long-term complications after clinical recovery from COVID-19, such as predisposition to the increased health risk in the post-COVID-19 era.
基金supported by the China Scholarship Council(CSC)Scholarship.
文摘Background:The greatest impact on profitability of a commercial beef operation is reproduction.However,in beef heifers,little is known about the vaginal and fecal microbiota with respect to their relationship with fertility.To this end,we followed heifers through gestation to examine the dynamics of vaginal and fecal microbial composition throughout pregnancy.Results:Heifers were exposed to an estrus synchronization protocol,observed over a 12-day period,artificially inseminated 12 h to 18 h after observed estrus,and subsequently exposed to bulls for a 50-day breeding season.Vaginal samples were taken at pre-breeding(n=72),during the first(n=72),and second trimester(n=72)for all individuals,and third trimester for individuals with confirmed pregnancies(n=56).Fecal samples were taken at prebreeding(n=32)and during the first trimester(n=32),including bred and open individuals.Next generation sequencing of the V4 region of the 16 S rRNA gene via the Illumina Mi Seq platform was applied to all samples.Shannon indices and the number of observed bacterial features were the same in fecal samples.However,significant differences in vaginal microbiome diversity between gestation stages were observed.No differences in beta-diversity were detected in vaginal or fecal samples regarding pregnancy status,but such differences were seen with fecal microbiome over time.Random Forest was developed to identify predictors of pregnancy status in vaginal(e.g.,Histophilus,Clostridiaceae,Campylobacter)and fecal(e.g.,Bacteroidales,Dorea)samples.Conclusions:Our study shows that bovine vaginal and fecal microbiome could be used as biomarkers of bovine reproduction.Further experiments are needed to validate these biomarkers and to examine their roles in a female’s ability to establish pregnancy.
基金funded by the National Key R&D Program of China(Grant no.2018YFC1406700)the National Natural Science Foundation of China(Grant no.41776198)the Basic Scientific Fund for National Public Research Institutes of China(Grant no.GY0219Q10)。
文摘One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being elevation of inorganic phosphate concentrations around feces depositions.The complex soil biochemistry in the region makes it difficult to define the causal factors of these changes using common research approaches.Here,we addressed the effects of phosphate alone on microbiome structure and dynamics over time by adding external phosphate to selected soils in the Antarctic region.We then analyzed the soil bacterial community composition and diversity using 16S rRNA amplicon sequencing and compared these data with phosphate levels.Parallel geochemical analysis revealed changes in nine soil geochemical factors upon phosphate addition,all of which were relevant to microbiome structure,with soil pH showing the highest correlation.Links between geochemical factors and composition were identified,as were interactions between bacterial taxa.Additionally,Sphingobacteriia,Sphingobacteriales and Chitinophagaceae were found to be more abundant in phosphate-treated soils.Co-occurrence network analysis revealed significantly increased levels of associations in all major network properties over time after phosphate supplementation.Therefore,we conclude phosphate addition has diverse effects on Antarctic soil microbiomes.
文摘Microorganisms are integral inhabitants of plants,playing a crucial role in plant growth,development,and health.The composition and diversity of microorganisms in plants can be influenced by several factors,including environmental factors such as soil type,temperature,and water availability.The plant microbiome serves essential functions,including nutrient acquisition,disease resistance,and stress tolerance,achieved through complex interactions between microorganisms and plants.Understanding these interactions and the impact of environmental factors can provide valuable insights into developing sustainable agricultural practices.The use of plant microbiomes in agriculture has the potential to improve crop yield,reduce fertilizer and pesticide use,and enhance soil health and sustainability,but scaling up these technologies poses several challenges.The potential benefits of using plant microbiomes in agriculture are significant and could revolutionize the industry.However,scaling up these technologies presents several challenges that require further research and innovation.In conclusion,studying plant microbiomes has the potential to bring about positive impacts for farmers,consumers,and the environment.
基金supported by the National Key Research and Development Program of China(2020YFA0608304,2020YFA0607603)the Natural Science Foundation of China(42176050,42276105,U1906216)+4 种基金the China Postdoctoral Science Foundation(2024M753347)the Shandong Province Postdoctoral Fund Project(SDBX2022030,SDCX-ZG-202400160)the Youth Innovation Promotion Association of CAS(2023220)the Taishan Scholar Foundation of Shandong Province(No.tsqn2024)the Ocean Negative Carbon Emissions(ONCE)Project.
文摘Macroalgae farming not only holds significant economic value but also contributes substantially to carbon sequestration,and therefore has gained intensified attention globally under climate change scenarios.However,its sustainability is increasingly threatened by anthropogenic and environmental changes.The health and resilience of macroalgae are intrinsically linked to their associated microbiomes,offering an untapped opportunity to enhance macroalgal farming through microbiome manipulation.In this review,we have summarized the current understanding of macroalgal microbiomes,highlighting critically underexplored microbial components,such as overlooked taxa,host specificity,and the environmental factors influencing microbiome composition,which hinder the development of effective microbiome engineering strategies.We critically evaluate existing microbiome manipulation approaches and their applications in enhancing macroalgal growth,resilience,carbon fixation,and biomass yield and assess their potential for improving macroalgal carbon sequestration.Finally,we propose a holistic framework that integrates multi-omics and metabolic modeling,microbial functional and environmental compatibility,high-throughput rapid isolation,and in vivo validation to bridge critical knowledge gaps and unlock the full potential of macroalgal microbiome engineering for sustainable,large-scale macroalgal farming.
基金supported by the National Natural Science Foundation of China(32325010,32070414,31821001)。
文摘Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome,the gut morphology is seldom independently considered and even often ignored.To address this research gap,we investigated a large-scale dataset of mammalian gut microbiomes,comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders.We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories(foregut/hindgut/simple,foregut/hindgut,functional ruminant/ruminant-like,and colon fermenter/cecum fermenter)and uncovered the synergistic effect between phylogeny and gut morphology.Moreover,we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches,as well as those within the same taxonomic order but with different gut morphologies.We also identified three enterotype indices—Fusobacterium,UCG-005,and Prevotella—which could predict the three gut morphology types of mammals:simple,foregut,and hindgut.These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.
基金supported by grants from the National Natural Science Foundation of China(Grant Nos.32100094 to Y.Wang and 42020104003 to Q.Huang)。
文摘Microbes play a crucial ecological role in soils,but the presence of relic DNA left by previous microorganisms can lead to inaccurate estimations of viable microbial function and diversity.To address this,we proposed a new method for removing relic DNA in soil using Benzonase endonuclease and compared it with propidium monoazide(PMA)and DNase I,which have been widely applied in viable microbiome studies.Unlike PMA,Benzonase does not require light activation and is suitable for use in opaque media such as soil.Therefore,its efficiency(40%-60%)in removing soil relic DNA was twice that of PMA(0-30%).Moreover,our results showed that Benzonase outperformed DNase I in most soils,probably due to its broader range of operating conditions compared to DNase I.In addition to higher relic DNA removal efficiency,Benzonase exhibited a weak impact on soil viable microbial communities.Subsequently,Benzonase was used to remove relic DNA in natural soils,and the results showed that relic DNA removal led to an approximately 10%reduction in microbial diversity and richness on average.Notably,it caused significant changes in the relative abundance of specific taxa,such as Bacillus and Sphingomonas.These findings reveal disparities between total and viable microbiomes in soils.Our study not only provides a reliable method for soil relic DNA removal but also highlights the necessity of relic DNA removal for viable soil microbiome assessments,laying the methodological foundation for advancing soil microbial ecology research.
基金the European Union’s Horizon Europe 2020 Research and Innovation Program under the Marie Skłodowska-Curie(No.101106707)Generalitat de Catalunya through Consolidated Research Group 2021 SGR 01282 and from the CERCA program.
文摘Soils are not exempt from anthropogenic pollution,which can eventually cause disturbance of the microbial communities and areas without any kind of productivity.Among soil microbiota,bacteria play an important role in pollutant degradation,enabling them to thrive in contaminated sites.Given this,several techniques have been used to increase the number of pollutantdegrading bacteria in situ or for subsequent addition.Additionally,bacteriophages exhibit a high tolerance to pollutants and enhance bacterial metabolic activity through phage-encoded auxiliary metabolic genes(AMGs),thereby augmenting their skills for nutrient assimilation,resistance to phage infection,antibiotic resistance,heavy metal resistance,and degradation of pesticides and xenobiotics,among others.Several phage-encoded AMGs have been described during the last few years,but their diversity,distribution,and function have not been extensively explored,warranting further studies.Here,we highlight soil microbiome interactions,especially bacterium and phage interactions to understand this unexplored world with a high potential for restoring polluted soils.
基金US Department of Agriculture(INFEWS/T1:AWD1006334)US Department of Energy(DE-EE0009494).
文摘Regulating electron transfer in predominantly fermentative microbiomes has broad implications in environmental,chemical,food,and medical fields.Here we demonstrate electrochemical control in fermenting food waste,digestate,and wastewater to improve lactic acid production.We hypothesize that applying anodic potential will expedite and direct fermentation towards lactic acid.Continued operation that introduced epi/endophytic communities(Lactococcus,Lactobacillus,Weissella)to pure culture Lactiplantibacillus plantarum reactors with static electrodes was associated with the loss of anode-induced process intensification despite 80%L.plantarum retention.Employing fluidized electrodes discouraged biofilm formation and extended electrode influence to planktonic gram-positive fermenters using mediated extracellular electron transfer.While short-term experiments differentially enriched Lactococcus and Klebsiella spp.,longer-term operations indicated convergent microbiomes and product spectra.These results highlight a functional resilience of environmental fermentative microbiomes to perturbations in redox potential,underscoring the need to better understand electrode induced polymicrobial interactions and physiological impacts to engineer tunable open-culture or synthetic consortia.
基金funded by the Hainan Provincial Natural Science Foundation of China(422RC744)Youth Innovation Promotion Association of Chinese Academy of Sciences(2020363)the“One Belt and One Road”Science and Technology Cooperation Special Program of the International Partnership Program of the Chinese Academy of Sciences(Grant No.183446KYSB20200016).
文摘Despite the growing awareness on the importance of gut microbiomes,understanding marine mammal gut microbiomes remains limited due to difficulties in sampling.Spotted dolphins(Stenella attenuata)are widely spread oceanic cetaceans,and there is a gap in knowledge regarding their gut microbiology.In this study,we opportunistically collected samples from both wild and human-cared spotted dolphins in the southern waters of Hainan Island,China.This provided the opportunity to examine the composition and diversity of the gut microbial communities of this cetacean species.Since these dolphins inhabit a similar water environment,different food sources might be the primary factor distinguishing the gut microbiomes of wild and human-cared populations,offering valuable experimental material to investigate potential differences in gut microbial community structure among marine mammals in similar environments but with varying food sources.We found that the gastrointestinal microbial community structure of wild and human-cared dolphins demonstrated significant differences,both overall and at specific locations.However,no significant difference was observed in the microbial diversity of their gastrointestinal tracts,indicating that the disparities primarily lie in microbiota composition.Additionally,we detected numerous potentially pathogenic bacteria,suggesting a comprehensive future study of marine mammal gut microbiology.Such a study might involve determining health indicator factors associated with these microbiomes.Our study not only supplements information on the gut microbiology of spotted dolphins but also delves into the similarities and differences in gastrointestinal microbial communities within the same marine mammal species when food source variations play a significant role in their lives.
基金Supported by WBE Liver Foundation,No.WBE20220182022 Young and Middle-aged Talents Incubation Project(Youth Innovation)of Beijing Youan Hospital,Capital Medical University,No.BJYAYY-YN-2022-092023 Young and Middle-aged Talents Incubation Project(Youth Innovation)of Beijing Youan Hospital,Capital Medical University,No.BJYAYYYN2023-14.
文摘BACKGROUND Autoimmune liver diseases,including primary biliary cholangitis(PBC),autoi-mmune hepatitis(AIH),and their overlap syndrome(OS),involve immune-mediated liver injury,with OS occurring in 1.2%-25%of PBC patients.OS carries a higher risk of cirrhosis,hepatocellular carcinoma,and reduced survival.While its pathogenesis remains unclear,gut microbiota dysbiosis and serum metabolite alterations may play key roles.This study uses 16S rRNA sequencing and liquid chromatography-mass spec-trometry(LC-MS)metabolomics to compare gut microbiota and serum metabolites among PBC,AIH,and OS patients,and explores their associations with liver function.AIM To differentiate OS from PBC and AIH based on gut microbiota,serum metabolites,and liver function.METHODS Gut microbiota profiles were analyzed using 16S rRNA sequencing,while untargeted serum metabolomics was conducted via LC-MS.Comparative analyses were performed to identify differences in microbial composition and serum metabolite levels among PBC,AIH,and OS groups.Correlation analyses and network visualization tech-niques were applied to elucidate the interactions among liver function parameters,gut microbiota,and serum metabolites in OS patients.RESULTS Compared to patients with PBC or AIH,OS patients demonstrated significantly reduced microbial diversity and richness.Notable taxonomic shifts included decreased abundances of Firmicutes,Bacteroidetes,and Actinobacteria,alongside increased levels of Proteobacteria and Verrucomicrobia.Distinct serum metabolites,such as pentadecanoic acid and aminoimidazole carboxamide ribonucleotide,were identified in OS patients.Correlation analysis revealed that aspartate aminotransferase(AST)levels were negatively associated with the bacterial genus Fusicatenibacter and the metabolite L-Tyrosine.A microbial-metabolite network diagram further confirmed a strong association between Fusicatenibacter and L-Tyrosine in OS patients.CONCLUSION OS patients show decreased gut microbiota diversity and unique serum metabolites.Multi-omics linked AST,Fusicatenibacter,and L-Tyrosine,revealing OS mechanisms and diagnostic potential.
基金Supported by the Zhejiang Provincial Natural Science Foundation,No.LZ22H270001.
文摘BACKGROUND Hepatic fibrosis(HF)represents a pivotal stage in the progression and potential reversal of cirrhosis,underscoring the importance of early identification and therapeutic intervention to modulate disease trajectory.AIM To explore the complex relationship between chronic hepatitis B(CHB)-related HF and gut microbiota to identify microbiota signatures significantly associated with HF progression in CHB patients using advanced machine learning algorithms.METHODS This study included patients diagnosed with CHB and classified them into HF and non-HF groups based on liver stiffness measurements.The HF group was further subdivided into four subgroups:F1,F2,F3,and F4.Data on clinical indicators were collected.Stool samples were collected for 16S rRNA sequencing to assess the gut microbiome.Microbiota diversity,relative abundance,and linear discriminant analysis effect size(LEfSe)were analyzed in different groups.Correlation analysis between clinical indicators and the relative abundance of gut microbiota was performed.The random forest and eXtreme gradient boosting algorithms were used to identify key differential gut microbiota.The Shapley additive explanations were used to evaluate microbiota importance.RESULTS Integrating the results from univariate analysis,LEfSe,and machine learning,we identified that the presence of Dorea in gut microbiota may be a key feature associated with CHB-related HF.Dorea possibly serves as a core differential feature of the gut microbiota that distinguishes HF from non-HF patients,and the presence of Dorea shows significant variations across different stages of HF(P<0.05).The relative abundance of Dorea significantly decreases with increasing HF severity(P=0.041).Moreover,the gut microbiota composition in patients with different stages of HF was found to correlate with several liver function indicators,such asγ-glutamyl transferase,alkaline phosphatase,total bilirubin,and the aspartate aminotransferase/alanine transaminase ratio(P<0.05).The associated pathways were predominantly enriched in biosynthesis,degradation/utilization/assimilation,generation of precursors,metabolites,and energy,among other categories.CONCLUSION HF affects the composition of the gut microbiota,indicating that the gut microbiota plays a crucial role in its pathophysiological processes.The abundance of Dorea varies significantly across various stages of HF,making it a potential microbial marker for identifying HF onset and progression.
基金This work was financially supported by National Natural Science Foundation of China （Grant No. 81771027）.
文摘Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms help human body against invasion of undesirable stim- ulation outside. However, imbalance of microbial flora contributes to oral diseases and systemic diseases. Oral microbiomes play an important role in the human microbial community and human health. The use of recently developed molecular methods has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Studies in oral microbiomes and their interactions with microbiomes in variable body sites and variable health condition are critical in our cognition of our body and how to make effect on human health improvement.
