Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor.An economical solid carbon source was developed by composition of polyvinyl alcohol,sodium alginate,and corncob...Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor.An economical solid carbon source was developed by composition of polyvinyl alcohol,sodium alginate,and corncob,which was utilized as external carbon source in the anaerobic anoxic oxic(AAO)-biofilter for the treatment of low carbon-to-nitrogen ratio domestic sewage,and the nitrogen removal was remarkably improved from 63.2%to 96.5%.Furthermore,the effluent chemical oxygen demand maintained at 35 mg/L or even lower,and the total nitrogenwas reduced to less than 2mg/L.Metagenomic analysis demonstrated that the microbial communities responsible for potential denitrification and organic matter degradation in both AAO and the biofilter reactors were mainly composed of Proteobacteria and Bacteroides,respectively.The solid carbon source addition resulted in relatively high abundance of functional enzymes responsible for NO_(3)^(−)-N to NO_(2)^(−)-N con-version in both AAO and the biofilter reactors,thus enabled stable reaction.The carbon source addition during glycolysis primarily led to the increase of genes associated with the metabolic conversion of fructose 1.6P2 to glycerol-3P The reactor maintained high abun-dance of genes related to the tricarboxylic acid cycle,and then guaranteed efficient carbon metabolism.The results indicate that the composite carbon source is feasible for denitri-fication enhancement of AAO-biofilter,which contribute to the theoretical foundation for practical nitrogen removal application.展开更多
Limitations regarding phosphorus(P)are widespread in ecosystems.Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetla...Limitations regarding phosphorus(P)are widespread in ecosystems.Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetlands.In this study,the Beidagang wetland,Baodi paddy field,and Dahuangpu wetland in Tianjin,China were chosen as representatives of the coastal wetland(B),constructed wetland(R),and swampy wetland(W),respectively.Sequential P extraction and metagenomics approaches were adopted to explore the soil P fraction and microbially regulated P cycle.Proteobacteria were the predominant microbes-related soil P cycle.IMPA,gph,rsbU_P,ugpQ,and glpK genes were dominant in organic P(Po)mineralization,while gcd,ppa,and ppx genes were dominant in inorganic P(Pi)solubilization.The salinity,NO_(3)^(-)-N concentration,the ratio of total carbon to total nitrogen(TC/TN),total carbon(TC),and the ratio of soil organic carbon to total P(SOC/TP)were the co-drivers of microbially mediated P cycle processes.Microbial network complexity-relate P cycle was the lowest in the coastal wetland.Salinity and NO_(3)^(-)-N exhibited a significant negative relation to the abundance of most genes-relate Pi solubilization and a remarkable positive correlation with the abundance of many genes-relate Po mineralization.These findings demonstrated that Po mineralization tended to occur in habitats with high salinity and nutrient imbalances,whereas the dissolution of Pi was prone to occur in low-salinity environments with relatively balanced soil nutrients.This study improves understanding of how salinity and soil nutrients jointly shape microbial-regulated soil P cycle in different types of wetlands.展开更多
There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine.The effectiveness of dust mitigation strategies such as oil sprinkling,to decrease risk of airborne virus transmi...There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine.The effectiveness of dust mitigation strategies such as oil sprinkling,to decrease risk of airborne virus transmission are unknown.Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents.Air particles were collected from swine buildings using high-volume air samplers.Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by highthroughput sequencing.Porcine astroviruses group 2 were common(from 102 to 105 genomic copies per cubic meter of air or gc/m^(3),93%positivity)while no norovirus genogroup II was recovered from air samples.Porcine torque teno sus virus were detected by qPCR in low concentrations(from 101 to 102 gc/m^(3),47%positivity).Among the identified viral families by metagenomics analysis,Herelleviridae,Microviridae,Myoviridae,Podoviridae,and Siphoviridae were dominant.The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m^(3) among the samples taken for the present study(97%positivity)and banked samples from5-and 15-year old studies(89%positivity).According to the present study,both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.展开更多
Erythromycin fermentation residue(EFR)represents a typical hazardous waste produced by the microbial pharmaceutical industry.Although electrolysis is promising for EFR disposal,its microbial threats remain unclear.Her...Erythromycin fermentation residue(EFR)represents a typical hazardous waste produced by the microbial pharmaceutical industry.Although electrolysis is promising for EFR disposal,its microbial threats remain unclear.Herein,metagenomics was coupled with the random forest technique to decipher the antibiotic resistance patterns of electrochemically treated EFR.Results showed that 95.75%of erythromycin could be removed in 2 hr.Electrolysis temporarily influenced EFRmicrobiota,where the relative abundances of Proteobacteria and Actinobacteria increased,while those of Fusobacteria,Firmicutes,and Bacteroidetes decreased.A total of 505 antibiotic resistance gene(ARG)subtypes encoding resistance to 21 antibiotic types and 150 mobile genetic elements(MGEs),mainly including plasmid(72)and transposase(52)were assembled in EFR.Significant linear regression models were identified among microbial richness,ARG subtypes,and MGE numbers(r^(2)=0.50-0.81,p<0.001).Physicochemical factors of EFR(Total nitrogen,total organic carbon,protein,and humus)regulated ARG and MGE assembly(%IncMSE value=5.14-14.85).The core ARG,MGE,and microbe sets(93.08%-99.85%)successfully explained 89.71%-92.92%of total ARG and MGE abundances.Specifically,gene aph(3 )-I,transposase tnpA,and Mycolicibacterium were the primary drivers of the resistance dissemination system.This study also proposes efficient resistance mitigation measures,and provides recommendations for future management of antibiotic fermentation residue.展开更多
With the rapid development of molecular biology technology,especially the application of metagenomics,many challenges in groundwater microbial research have been overcome.Metagenomics has enabled the exploration of th...With the rapid development of molecular biology technology,especially the application of metagenomics,many challenges in groundwater microbial research have been overcome.Metagenomics has enabled the exploration of the diversity of unculturable microorganisms in groundwater.This paper reviews macro genomics 16S rRNA and metagenomics sequencing data,highlighting recent applications of metagenomics in investigating groundwater microbial communities.It also examines the relationship between microbial diversity and environmental factors,the identification of functional microbial groups,the role of microorganisms in groundwater pollution remediation,and their contribution to the hydrogeochemi-cal cycle.Finally,it provide insights into future research directions in groundwater microbiology.展开更多
There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating me...There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating metabolic processes,and is even regarded as an endocrine organ.However,traditional culture methods are very limited for identifying microbes.With the application of molecular biologic technology in the field of the intestinal microbiome,especially metagenomic sequencing of the next-generation sequencing technology,progress has been made in the study of the human intestinal microbiome.Metagenomics can be used to study intestinal microbiome diversity and dysbiosis,as well as its relationship to health and disease.Moreover,functional metagenomics can identify novel functional genes,microbial pathways,antibiotic resistance genes,functional dysbiosis of the intestinal microbiome,and determine interactions and co-evolution between microbiota and host,though there are still some limitations.Metatranscriptomics,metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome.This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects.The limitations of metagenomics to be overcome are also discussed.Metatranscriptomics,metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.展开更多
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in...A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.展开更多
East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a...East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.展开更多
Infectious diseases are a great threat to human health.Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases.Metagenomics next-generation sequencing(mNGS)is an un...Infectious diseases are a great threat to human health.Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases.Metagenomics next-generation sequencing(mNGS)is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample.With the development of sequencing and bioinformatics technologies,mNGS is moving from research to clinical application,which opens a new avenue for pathogen detection.Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases,especially in difficult-to-detect,rare,and novel pathogens.However,there are several hurdles in the clinical application of mNGS,such as:(1)lack of universal workflow validation and quality assurance;(2)insensitivity to high-host background and low-biomass samples;and(3)lack of standardized instructions for mass data analysis and report interpretation.Therefore,a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases.This review briefly introduces the history of next-generation sequencing,mainstream sequencing platforms,and mNGS workflow,and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.展开更多
Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance reco...Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.展开更多
The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Bar...The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Barrésyndrome due to autonomic disturbance,symmetrical bulbar palsy,and lower-motor-nerve damage in the extremities;her symptoms continued to worsen after hormone and immunoglobulin therapy.Later,parasitic larvae were found in the patient’s gastric fluid,and metagenomic next generation sequencing(mNGS)detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms.The patient was diagnosed with disseminated strongyloidiasis.The patient was given albendazole for anthelmintic treatment,but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden.In recent years,mNGS has been increasingly used in clinical practice,and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas.Especially during the corona virus disease 2019 pandemic,mNGS technology has irreplaceable value in identifying the source of infection.展开更多
Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the mai...Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the main pathogen of diarrhea.In China,the fecal virome of children with diarrhea has been rarely studied.Using an unbiased viral metagenomics approach,we analyzed the fecal virome in children with diarrhea.Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae,Astroviridae,Caliciviridae,Parvoviridae,Picornaviridae,and Reoviridae.Among them,the family of Caliciviridae accounts for the largest proportion of 78.42%,following with Adenoviridae(8.94%)and Picornaviridae(8.36%).In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea,the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus.This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.展开更多
Recent studies have declared that members of the ss DNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this s...Recent studies have declared that members of the ss DNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease(CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD.Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.展开更多
The human microbiota is made up of trillions of bacteria that live in the human being,whereas the microbiome is made up of the microbiota's genes and gene products.Bacteria have long been thought of as pathogens t...The human microbiota is made up of trillions of bacteria that live in the human being,whereas the microbiome is made up of the microbiota's genes and gene products.Bacteria have long been thought of as pathogens that eventually lead to human illness.Bacteria are increasingly recognized as generally beneficial commensal organisms and hence crucial to proper and healthy human development,thanks to breakthroughs in both cultivation-based approaches and the advent of metagenomics.This relatively new field of medical study has given more information on illnesses such as inflammatory bowel disease,obesity,metabolic and atopic disorders.However,there is a lot we don't know about the complexities of microbe-microbe and microbe-host interactions.Future work targeted at resolving crucial concerns about the early formation of the microbiome,in addition,what determines its dysbiosis,will most likely lead to long-term mitigation of health.In this article,review the research on prenatal and newborn microbiome modulations,the role of maternal and environmental variables on forming the newborn microbiome,and future issues and directions in the exciting new field of metagenomic medicine.展开更多
Background:Camels,known as the enduring“ships of the desert,”host a complex gut microbiota that plays a crucial role in their survival in extreme environments.However,amidst the fascinating discoveries about the cam...Background:Camels,known as the enduring“ships of the desert,”host a complex gut microbiota that plays a crucial role in their survival in extreme environments.However,amidst the fascinating discoveries about the camel gut microbiota,concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations.Indeed,the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria,which has worsened through gene transfer.Methods:This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel(Camelus ferus)gut microbiota and antibiotic resistance.Results:Samples from wild camels yielded varying amounts of raw and clean data,generating scaftigs and open reading frames.The camel fecal microbiome was dominated by bacteria(mainly Bacillota and Bacteriodota),followed by viruses,archaea,and eukaryota.The most abundant genera were the Bacteroides,Ruminococcus,and Clostridium.Functional annotation revealed enriched pathways in metabolism,genetic information processing,and cellular processes,with key pathways involving carbohydrate transport and metabolism,replication,and amino acid transport.CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases.Antibiotic resistance gene(ARG)analysis identified Bacillota and Bacteroidota as the main reservoirs,with vancomycin resistance genes being the most prevalent.This study identified three major resistance mechanisms:antibiotic target alteration,antibiotic target protection,and antibiotic efflux.Conclusion:These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance.展开更多
Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study r...Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study recruited one pregnant woman,who ingested Probio-M9 daily from 35 weeks of gestation to delivery.Feces of the mother-infant pair were regularly collected from one month before delivery to 6 months of infant's age for metagenomic sequencing.Probio-M9 genomes were mappable to all infant fecal samples,suggesting the ingested probiotics could be vertically transmitted from mother to infant.Infant-or mother-specific differential metabolic pathways were found between the maternal and infant's gut microbiome,implicating apparent differences in the intestinal metagenomic potential/function between the mother and the infant.In conclusion,maternal ingestion of Probio-M9 during the final weeks of gestation could deliver to the infant gut.The findings provided novel insights into shaping infant's gut microbiota.展开更多
Methylmercury(MeHg)is a potent neurotoxin and bioaccumulates in food webs.Microbial transformation of inorganic mercury(Hg)produces most of the MeHg in the marine environment.The gene pair hgcAB encodes for Hg methyla...Methylmercury(MeHg)is a potent neurotoxin and bioaccumulates in food webs.Microbial transformation of inorganic mercury(Hg)produces most of the MeHg in the marine environment.The gene pair hgcAB encodes for Hg methylation,a process predominantly attributed to anaerobic bacteria.However,recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns,although the mechanisms remain poorly understood.“Blue holes”are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles.Here,we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem.Yongle Blue Hole(YBH),currently the world’s deepest known blue hole,was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment.Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation,driven by abundant and diverse Deltaproteobacteria.In the suboxic intermediate layer,Nitrospina and Myxococcota dominated the Hg-methylating community.Furthermore,Hg methylators were found to have different lifestyles(free-living or particle-associated)and to occupy distinct ecological niches within the YBH.In addition,the contribution of sinking particles to Hg methylation,especially in the deep anoxic water column,was highlighted.Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments.The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.展开更多
Douchi is traditionally produced through natural fermentation without intentionally inoculated microorganisms.To improve the fermentation process,this study aimed to investigate the effects on microbiota and flavor du...Douchi is traditionally produced through natural fermentation without intentionally inoculated microorganisms.To improve the fermentation process,this study aimed to investigate the effects on microbiota and flavor during Douchi fermentation using selected autochthonous microorganisms,Bacillus amyloliquefaciens B9 and Pichia kudriavzevii Y18.Results showed that bacteria dominated the fermentation process,while fungi played a supplementary role.Genus-level analysis identified Bacillus as the most prevalent genus during fermentation,while Pichia surged on day 15 and reached peak relative abundance by day 22.During post-fermentation,the total content of volatile compounds increased by 126.91%,and the content of esters rose significantly to 1190.90μg/kg by day 30.Compared with day 0,six key volatile flavor compounds with odor activity values(OAV)exceeding 1 were newly produced,indicating that the inoculated microorganisms significantly contributed to their formation.Non-volatile metabolites exhibited varying trends,with their accumulations stabilizing in the later stages of fermentation.Notably,amino acids and dipeptides accumulated significantly during fermentation,enhancing the nutritional and flavor profiles of Douchi.The construction of the metabolic network highlighted that amino acid and carbohydrate metabolism were pivotal pathways for flavor enhancement during Douchi postfermentation.Furthermore,pyruvate and acetyl-CoA were critical in Douchi fermentation and acted as core intermediates for flavor compound production,participating in amino acid biosynthesis,the tricarboxylic acid cycle,and fatty acid biosynthesis.Additionally,Pichia played a role in the biosynthesis of γ-Aminobutyric acid.This study systematically explored the multidimensional characteristics of Douchi post-fermentation,bridging the gap between descriptive research and mechanism-driven fermentation control strategies.展开更多
Ciba chili are a distinctive chili condiment from southwestern China,those produced using single rehydration methods encounter challenges related to monotonous flavor and inconsistent quality.This study investigated t...Ciba chili are a distinctive chili condiment from southwestern China,those produced using single rehydration methods encounter challenges related to monotonous flavor and inconsistent quality.This study investigated the quality changes in Ciba chili over 0–28 days of natural fermentation.The physicochemical analysis revealed a significant decrease in pH,while total acidity and amino nitrogen content increased markedly.This indicates that fermentation effectively promoted acidification and increased the production of nitrogen compounds.Through untargeted metabolomics,2106 metabolites were identified and annotated.KEGG pathway analysis of the differential metabolites revealed that 2-oxoglutarate,a key intermediate in the tricarboxylic acid(TCA)cycle,serves as a crucial metabolic hub for the synthesis of flavor compounds.Moreover,gas chromatography-ion mobility spectrometry identified 52 Volatile organic compounds(VOCs),with substantial increases observed in alcohols,ketones,alkanes,pyrazines,and furans following fermentation,all contributing to the enhanced aroma of Ciba chili.Dominant microbial genera,including Lactiplantibacillus,Weissella,and Leuconostoc,were strongly associated with VOCs and metabolites,playing a pivotal role in flavor development.The results suggest that fermentation is an effective method for improving the quality and flavor of Ciba chili,demonstrating substantial potential for practical applications.展开更多
Daqu,a traditional fermentation starter produced by solid-state fermentation,is highly susceptible to environ-mental factors due to its open production environment.While Daqu is frequently infested by pests such as Tr...Daqu,a traditional fermentation starter produced by solid-state fermentation,is highly susceptible to environ-mental factors due to its open production environment.While Daqu is frequently infested by pests such as Tri-bolium castaneum,the impact of their internal microbiota on the Daqu microbial community remains unclear.The purpose of the present study was to elucidate their interaction effect.Therefore,metagenomic technology was applied for analyzing the microbiomes of Daqu produced across spring,summer,and autumn.The results showed that the quality of spring Daqu is superior to that of autumn and summer Daqu.Correlation analysis demon-strated that the impact of Daqu pests'(QC)internal microbiota on the microbial community structure of Daqu was significantly smaller than that of temperature and humidity,so the environmental temperature and humidity were the primary drivers shaping Daqu's microbial community structure.Metagenomic analysis identified the core microbiota within the pests,including bacteria such as Lactococcus garvieae,and Klebsiella pneumoniae,and fungi like Erysiphe pulchra and Fusarium avenaceum.Co-occurrence network and UpSet analyses indicated that only 13 microorganisms in summer Daqu may come from QC,and their abundance is extremely low.Microbial species shared between QC and summer Daqu accounted for over half of QC's total internal microbiota.These findings highlight that the microbial influence of the microbiota of QC on Daqu fermentation is minimal,whereas the Daqu environment significantly shapes the pests'microbiota.In conclusion,this study underscores the importance of environmental control in Daqu production,providing key insights for optimizing fermentation conditions.展开更多
基金supported by the Special Funds for Chengde national innovation demonstration area construction of science and technology special project sustainable development agenda(No.202104F001)the National Basic Research Program of China(No.2019YFC0408602).
文摘Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor.An economical solid carbon source was developed by composition of polyvinyl alcohol,sodium alginate,and corncob,which was utilized as external carbon source in the anaerobic anoxic oxic(AAO)-biofilter for the treatment of low carbon-to-nitrogen ratio domestic sewage,and the nitrogen removal was remarkably improved from 63.2%to 96.5%.Furthermore,the effluent chemical oxygen demand maintained at 35 mg/L or even lower,and the total nitrogenwas reduced to less than 2mg/L.Metagenomic analysis demonstrated that the microbial communities responsible for potential denitrification and organic matter degradation in both AAO and the biofilter reactors were mainly composed of Proteobacteria and Bacteroides,respectively.The solid carbon source addition resulted in relatively high abundance of functional enzymes responsible for NO_(3)^(−)-N to NO_(2)^(−)-N con-version in both AAO and the biofilter reactors,thus enabled stable reaction.The carbon source addition during glycolysis primarily led to the increase of genes associated with the metabolic conversion of fructose 1.6P2 to glycerol-3P The reactor maintained high abun-dance of genes related to the tricarboxylic acid cycle,and then guaranteed efficient carbon metabolism.The results indicate that the composite carbon source is feasible for denitri-fication enhancement of AAO-biofilter,which contribute to the theoretical foundation for practical nitrogen removal application.
基金supported by the National Natural Science Foundation of China(Nos.32271777,31500365,31770499,and 42303014)Tianjin Natural Science Foundation(Nos.12JCYBJC19700 and 18JCYBJC96500)+1 种基金Tianjin Science and Technology Support Program(Nos.23YFZCSN00100,15ZCZDSF00410,and 23YFZCSN00210)the Special Investigation of Technological Basic Resources(No.2021FY101002)。
文摘Limitations regarding phosphorus(P)are widespread in ecosystems.Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetlands.In this study,the Beidagang wetland,Baodi paddy field,and Dahuangpu wetland in Tianjin,China were chosen as representatives of the coastal wetland(B),constructed wetland(R),and swampy wetland(W),respectively.Sequential P extraction and metagenomics approaches were adopted to explore the soil P fraction and microbially regulated P cycle.Proteobacteria were the predominant microbes-related soil P cycle.IMPA,gph,rsbU_P,ugpQ,and glpK genes were dominant in organic P(Po)mineralization,while gcd,ppa,and ppx genes were dominant in inorganic P(Pi)solubilization.The salinity,NO_(3)^(-)-N concentration,the ratio of total carbon to total nitrogen(TC/TN),total carbon(TC),and the ratio of soil organic carbon to total P(SOC/TP)were the co-drivers of microbially mediated P cycle processes.Microbial network complexity-relate P cycle was the lowest in the coastal wetland.Salinity and NO_(3)^(-)-N exhibited a significant negative relation to the abundance of most genes-relate Pi solubilization and a remarkable positive correlation with the abundance of many genes-relate Po mineralization.These findings demonstrated that Po mineralization tended to occur in habitats with high salinity and nutrient imbalances,whereas the dissolution of Pi was prone to occur in low-salinity environments with relatively balanced soil nutrients.This study improves understanding of how salinity and soil nutrients jointly shape microbial-regulated soil P cycle in different types of wetlands.
文摘There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine.The effectiveness of dust mitigation strategies such as oil sprinkling,to decrease risk of airborne virus transmission are unknown.Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents.Air particles were collected from swine buildings using high-volume air samplers.Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by highthroughput sequencing.Porcine astroviruses group 2 were common(from 102 to 105 genomic copies per cubic meter of air or gc/m^(3),93%positivity)while no norovirus genogroup II was recovered from air samples.Porcine torque teno sus virus were detected by qPCR in low concentrations(from 101 to 102 gc/m^(3),47%positivity).Among the identified viral families by metagenomics analysis,Herelleviridae,Microviridae,Myoviridae,Podoviridae,and Siphoviridae were dominant.The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m^(3) among the samples taken for the present study(97%positivity)and banked samples from5-and 15-year old studies(89%positivity).According to the present study,both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.
基金supported by the Special Project of Basic Scientific Research Business of Central Public Welfare Scientific Research Institutes (No.2019YSKY-027).
文摘Erythromycin fermentation residue(EFR)represents a typical hazardous waste produced by the microbial pharmaceutical industry.Although electrolysis is promising for EFR disposal,its microbial threats remain unclear.Herein,metagenomics was coupled with the random forest technique to decipher the antibiotic resistance patterns of electrochemically treated EFR.Results showed that 95.75%of erythromycin could be removed in 2 hr.Electrolysis temporarily influenced EFRmicrobiota,where the relative abundances of Proteobacteria and Actinobacteria increased,while those of Fusobacteria,Firmicutes,and Bacteroidetes decreased.A total of 505 antibiotic resistance gene(ARG)subtypes encoding resistance to 21 antibiotic types and 150 mobile genetic elements(MGEs),mainly including plasmid(72)and transposase(52)were assembled in EFR.Significant linear regression models were identified among microbial richness,ARG subtypes,and MGE numbers(r^(2)=0.50-0.81,p<0.001).Physicochemical factors of EFR(Total nitrogen,total organic carbon,protein,and humus)regulated ARG and MGE assembly(%IncMSE value=5.14-14.85).The core ARG,MGE,and microbe sets(93.08%-99.85%)successfully explained 89.71%-92.92%of total ARG and MGE abundances.Specifically,gene aph(3 )-I,transposase tnpA,and Mycolicibacterium were the primary drivers of the resistance dissemination system.This study also proposes efficient resistance mitigation measures,and provides recommendations for future management of antibiotic fermentation residue.
基金funded by Basic Research Funds of Chinese Academy of Geological Sciences(CSJ-2021-10).
文摘With the rapid development of molecular biology technology,especially the application of metagenomics,many challenges in groundwater microbial research have been overcome.Metagenomics has enabled the exploration of the diversity of unculturable microorganisms in groundwater.This paper reviews macro genomics 16S rRNA and metagenomics sequencing data,highlighting recent applications of metagenomics in investigating groundwater microbial communities.It also examines the relationship between microbial diversity and environmental factors,the identification of functional microbial groups,the role of microorganisms in groundwater pollution remediation,and their contribution to the hydrogeochemi-cal cycle.Finally,it provide insights into future research directions in groundwater microbiology.
基金Supported by National Basic Research Program(973 Program)of China,No.2013CB531403
文摘There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating metabolic processes,and is even regarded as an endocrine organ.However,traditional culture methods are very limited for identifying microbes.With the application of molecular biologic technology in the field of the intestinal microbiome,especially metagenomic sequencing of the next-generation sequencing technology,progress has been made in the study of the human intestinal microbiome.Metagenomics can be used to study intestinal microbiome diversity and dysbiosis,as well as its relationship to health and disease.Moreover,functional metagenomics can identify novel functional genes,microbial pathways,antibiotic resistance genes,functional dysbiosis of the intestinal microbiome,and determine interactions and co-evolution between microbiota and host,though there are still some limitations.Metatranscriptomics,metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome.This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects.The limitations of metagenomics to be overcome are also discussed.Metatranscriptomics,metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.
基金financially supported by the National Natural Science Foundation of China,No.32002235(to MT)the Science and Technology Foundation of Taian of Shandong Province,No.2020NS216(to XL)。
文摘A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
文摘East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.
基金supported by the Medicine and Health,Science and Technology Plan Project of Zhejiang(Nos.2020KY1009 and 2021KY387)the Jinhua Science and Technology Planning Project Social Development Key Project(No.2021-3-072),China.
文摘Infectious diseases are a great threat to human health.Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases.Metagenomics next-generation sequencing(mNGS)is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample.With the development of sequencing and bioinformatics technologies,mNGS is moving from research to clinical application,which opens a new avenue for pathogen detection.Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases,especially in difficult-to-detect,rare,and novel pathogens.However,there are several hurdles in the clinical application of mNGS,such as:(1)lack of universal workflow validation and quality assurance;(2)insensitivity to high-host background and low-biomass samples;and(3)lack of standardized instructions for mass data analysis and report interpretation.Therefore,a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases.This review briefly introduces the history of next-generation sequencing,mainstream sequencing platforms,and mNGS workflow,and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
基金supported by the National Key Research and Development Program of China (No.2021YFC3201504)the National Natural Science Foundations of China (No.52000140)the Social Development Program of Science and Technology Committee Foundations of Shanghai (No.22dz1209200)。
文摘Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.
文摘The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Barrésyndrome due to autonomic disturbance,symmetrical bulbar palsy,and lower-motor-nerve damage in the extremities;her symptoms continued to worsen after hormone and immunoglobulin therapy.Later,parasitic larvae were found in the patient’s gastric fluid,and metagenomic next generation sequencing(mNGS)detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms.The patient was diagnosed with disseminated strongyloidiasis.The patient was given albendazole for anthelmintic treatment,but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden.In recent years,mNGS has been increasingly used in clinical practice,and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas.Especially during the corona virus disease 2019 pandemic,mNGS technology has irreplaceable value in identifying the source of infection.
基金supported by Jiangsu Provincial Key Research and Development Projects No.BE2017693National Natural Science Foundation of China No.81741062
文摘Diarrhea is the third leading cause of death in developing countries in children under the age of five.About half a million children die of diarrhea every year,most of which in developing countries.Viruses are the main pathogen of diarrhea.In China,the fecal virome of children with diarrhea has been rarely studied.Using an unbiased viral metagenomics approach,we analyzed the fecal virome in children with diarrhea.Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae,Astroviridae,Caliciviridae,Parvoviridae,Picornaviridae,and Reoviridae.Among them,the family of Caliciviridae accounts for the largest proportion of 78.42%,following with Adenoviridae(8.94%)and Picornaviridae(8.36%).In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea,the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus.This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.
基金financially supported by the "2014 AgriX" Project Found of Shanghai Jiao Tong University(No. AF1500028/001)
文摘Recent studies have declared that members of the ss DNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease(CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD.Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.
文摘The human microbiota is made up of trillions of bacteria that live in the human being,whereas the microbiome is made up of the microbiota's genes and gene products.Bacteria have long been thought of as pathogens that eventually lead to human illness.Bacteria are increasingly recognized as generally beneficial commensal organisms and hence crucial to proper and healthy human development,thanks to breakthroughs in both cultivation-based approaches and the advent of metagenomics.This relatively new field of medical study has given more information on illnesses such as inflammatory bowel disease,obesity,metabolic and atopic disorders.However,there is a lot we don't know about the complexities of microbe-microbe and microbe-host interactions.Future work targeted at resolving crucial concerns about the early formation of the microbiome,in addition,what determines its dysbiosis,will most likely lead to long-term mitigation of health.In this article,review the research on prenatal and newborn microbiome modulations,the role of maternal and environmental variables on forming the newborn microbiome,and future issues and directions in the exciting new field of metagenomic medicine.
基金supported by the Project of Fund for Stable Support to Agricultural Sci-Tech Renovation of XAAS(grant number:xjnkywdzc-2023005-6)Key Laboratory of Biological Resources and Ecology of the Pamir Plateau,Xinjiang(grant number:XJDX1714-2021-01)+1 种基金The Major Science and Technology Project of Xinjiang Uygur Autonomous Region(grant number:2022A02005-4-2)Xinjiang Uygur Autonomous Region Rural Revitalization Industry Development Science and Technology Action Project(grant number:2022NC073).
文摘Background:Camels,known as the enduring“ships of the desert,”host a complex gut microbiota that plays a crucial role in their survival in extreme environments.However,amidst the fascinating discoveries about the camel gut microbiota,concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations.Indeed,the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria,which has worsened through gene transfer.Methods:This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel(Camelus ferus)gut microbiota and antibiotic resistance.Results:Samples from wild camels yielded varying amounts of raw and clean data,generating scaftigs and open reading frames.The camel fecal microbiome was dominated by bacteria(mainly Bacillota and Bacteriodota),followed by viruses,archaea,and eukaryota.The most abundant genera were the Bacteroides,Ruminococcus,and Clostridium.Functional annotation revealed enriched pathways in metabolism,genetic information processing,and cellular processes,with key pathways involving carbohydrate transport and metabolism,replication,and amino acid transport.CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases.Antibiotic resistance gene(ARG)analysis identified Bacillota and Bacteroidota as the main reservoirs,with vancomycin resistance genes being the most prevalent.This study identified three major resistance mechanisms:antibiotic target alteration,antibiotic target protection,and antibiotic efflux.Conclusion:These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance.
基金supported by Science and Technology Major Projects of Inner Mongolia Autonomous Region(2021ZD0014)。
文摘Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study recruited one pregnant woman,who ingested Probio-M9 daily from 35 weeks of gestation to delivery.Feces of the mother-infant pair were regularly collected from one month before delivery to 6 months of infant's age for metagenomic sequencing.Probio-M9 genomes were mappable to all infant fecal samples,suggesting the ingested probiotics could be vertically transmitted from mother to infant.Infant-or mother-specific differential metabolic pathways were found between the maternal and infant's gut microbiome,implicating apparent differences in the intestinal metagenomic potential/function between the mother and the infant.In conclusion,maternal ingestion of Probio-M9 during the final weeks of gestation could deliver to the infant gut.The findings provided novel insights into shaping infant's gut microbiota.
基金supported by The University of Melbourne’s Research Computing Services and the Petascale Campus Initiative.
文摘Methylmercury(MeHg)is a potent neurotoxin and bioaccumulates in food webs.Microbial transformation of inorganic mercury(Hg)produces most of the MeHg in the marine environment.The gene pair hgcAB encodes for Hg methylation,a process predominantly attributed to anaerobic bacteria.However,recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns,although the mechanisms remain poorly understood.“Blue holes”are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles.Here,we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem.Yongle Blue Hole(YBH),currently the world’s deepest known blue hole,was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment.Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation,driven by abundant and diverse Deltaproteobacteria.In the suboxic intermediate layer,Nitrospina and Myxococcota dominated the Hg-methylating community.Furthermore,Hg methylators were found to have different lifestyles(free-living or particle-associated)and to occupy distinct ecological niches within the YBH.In addition,the contribution of sinking particles to Hg methylation,especially in the deep anoxic water column,was highlighted.Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments.The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.
基金supported by the National Key Research and Devel-opment Program of the Ministry of Science and Technology(Project No.2022YFE0120800).
文摘Douchi is traditionally produced through natural fermentation without intentionally inoculated microorganisms.To improve the fermentation process,this study aimed to investigate the effects on microbiota and flavor during Douchi fermentation using selected autochthonous microorganisms,Bacillus amyloliquefaciens B9 and Pichia kudriavzevii Y18.Results showed that bacteria dominated the fermentation process,while fungi played a supplementary role.Genus-level analysis identified Bacillus as the most prevalent genus during fermentation,while Pichia surged on day 15 and reached peak relative abundance by day 22.During post-fermentation,the total content of volatile compounds increased by 126.91%,and the content of esters rose significantly to 1190.90μg/kg by day 30.Compared with day 0,six key volatile flavor compounds with odor activity values(OAV)exceeding 1 were newly produced,indicating that the inoculated microorganisms significantly contributed to their formation.Non-volatile metabolites exhibited varying trends,with their accumulations stabilizing in the later stages of fermentation.Notably,amino acids and dipeptides accumulated significantly during fermentation,enhancing the nutritional and flavor profiles of Douchi.The construction of the metabolic network highlighted that amino acid and carbohydrate metabolism were pivotal pathways for flavor enhancement during Douchi postfermentation.Furthermore,pyruvate and acetyl-CoA were critical in Douchi fermentation and acted as core intermediates for flavor compound production,participating in amino acid biosynthesis,the tricarboxylic acid cycle,and fatty acid biosynthesis.Additionally,Pichia played a role in the biosynthesis of γ-Aminobutyric acid.This study systematically explored the multidimensional characteristics of Douchi post-fermentation,bridging the gap between descriptive research and mechanism-driven fermentation control strategies.
基金funded by several projects,including the key research and development project from the Sichuan Provincial Education Department[grant number 23ZDYF3065]the research and development initiative from the Sichuan Province Science and Technology Department[grant number 2023YFS0490,2023ZHCG0078]+3 种基金the Key Laboratory of Culinary Science at Sichuan Provincial Universities Department[grant number PRKX 2024Z02]the Sichuan Cuisine Development Research Center[grant number CC24Z24]Chengdu University Meat Processing Key Laboratory of Sichuan Province Department[grant number 21-R-12]Key Laboratory of Sichuan Cuisine Artificial Intelligence Department[grant number CR24ZX01].
文摘Ciba chili are a distinctive chili condiment from southwestern China,those produced using single rehydration methods encounter challenges related to monotonous flavor and inconsistent quality.This study investigated the quality changes in Ciba chili over 0–28 days of natural fermentation.The physicochemical analysis revealed a significant decrease in pH,while total acidity and amino nitrogen content increased markedly.This indicates that fermentation effectively promoted acidification and increased the production of nitrogen compounds.Through untargeted metabolomics,2106 metabolites were identified and annotated.KEGG pathway analysis of the differential metabolites revealed that 2-oxoglutarate,a key intermediate in the tricarboxylic acid(TCA)cycle,serves as a crucial metabolic hub for the synthesis of flavor compounds.Moreover,gas chromatography-ion mobility spectrometry identified 52 Volatile organic compounds(VOCs),with substantial increases observed in alcohols,ketones,alkanes,pyrazines,and furans following fermentation,all contributing to the enhanced aroma of Ciba chili.Dominant microbial genera,including Lactiplantibacillus,Weissella,and Leuconostoc,were strongly associated with VOCs and metabolites,playing a pivotal role in flavor development.The results suggest that fermentation is an effective method for improving the quality and flavor of Ciba chili,demonstrating substantial potential for practical applications.
基金supported by the National Natural Science Foundation of China(32472321)the Natural Science Foundation of Tianjin(25JJJJC0021)+1 种基金Innovative Research Team of Shanxi Province,Key Research and Development Projects of Shanxi Province(202402130501001)Key Technology Research Project of Taiyuan(2024TYJB0146).
文摘Daqu,a traditional fermentation starter produced by solid-state fermentation,is highly susceptible to environ-mental factors due to its open production environment.While Daqu is frequently infested by pests such as Tri-bolium castaneum,the impact of their internal microbiota on the Daqu microbial community remains unclear.The purpose of the present study was to elucidate their interaction effect.Therefore,metagenomic technology was applied for analyzing the microbiomes of Daqu produced across spring,summer,and autumn.The results showed that the quality of spring Daqu is superior to that of autumn and summer Daqu.Correlation analysis demon-strated that the impact of Daqu pests'(QC)internal microbiota on the microbial community structure of Daqu was significantly smaller than that of temperature and humidity,so the environmental temperature and humidity were the primary drivers shaping Daqu's microbial community structure.Metagenomic analysis identified the core microbiota within the pests,including bacteria such as Lactococcus garvieae,and Klebsiella pneumoniae,and fungi like Erysiphe pulchra and Fusarium avenaceum.Co-occurrence network and UpSet analyses indicated that only 13 microorganisms in summer Daqu may come from QC,and their abundance is extremely low.Microbial species shared between QC and summer Daqu accounted for over half of QC's total internal microbiota.These findings highlight that the microbial influence of the microbiota of QC on Daqu fermentation is minimal,whereas the Daqu environment significantly shapes the pests'microbiota.In conclusion,this study underscores the importance of environmental control in Daqu production,providing key insights for optimizing fermentation conditions.
