Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging,yet there is limited understanding of gut microbiome variation in advanced age.Here,we performed a metagenom...Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging,yet there is limited understanding of gut microbiome variation in advanced age.Here,we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years,with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations.In addition to two adult-like enterotypes dominated by Bacteroides(ET-Bacteroides)and Prevotella(ET-Prevotella),we identified a novel enterotype dominated by Escherichia(ET-Escherichia),whose prevalence increased in advanced age.Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus(T2DM)or diet.We characterized the distinct taxonomic and functional profiles of ET-Escherichia,and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype,as well as the lowest species diversity.In addition,we carried out a series of correlation analyses and co-abundance network analyses,which showed that several factors were likely linked to the overabundance of Escherichia members,including advanced age,vegetable intake,and fruit intake.Overall,our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population.Considering the different age distribution of each enterotype,these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.展开更多
Background Dairy cows’lactation performance is the outcome of the crosstalk between ruminal microbial metabo-lism and host metabolism.However,it is still unclear to what extent the rumen microbiome and its metabolite...Background Dairy cows’lactation performance is the outcome of the crosstalk between ruminal microbial metabo-lism and host metabolism.However,it is still unclear to what extent the rumen microbiome and its metabolites,as well as the host metabolism,contribute to regulating the milk protein yield(MPY).Methods The rumen fluid,serum and milk of 12 Holstein cows with the same diet(45%coarseness ratio),parity(2–3 fetuses)and lactation days(120–150 d)were used for the microbiome and metabolome analysis.Rumen metabolism(rumen metabolome)and host metabolism(blood and milk metabolome)were connected using a weighted gene co-expression network(WGCNA)and the structural equation model(SEM)analyses.Results Two different ruminal enterotypes,with abundant Prevotella and Ruminococcus,were identified as type1 and type2.Of these,a higher MPY was found in cows with ruminal type2.Interestingly,[Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae(the differential bacteria)were the hub genera of the network.In addition,differential ruminal,serum and milk metabolome between enterotypes were identified,where the cows with type2 had higher L-tyrosine of rumen,ornithine and L-tryptophan of serum,and tetrahydroneopterin,palmitoyl-L-carnitine,S-lactoylglutathione of milk,which could provide more energy and substrate for MPY.Further,based on the identi-fied modules of ruminal microbiome,as well as ruminal serum and milk metabolome using WGCNA,the SEM analysis indicated that the key ruminal microbial module1,which contains the hub genera of the network([Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae)and high abundance of bacteria(Prevotella and Ruminococcus),could regulate the MPY by module7 of rumen,module2 of blood,and module7 of milk,which contained L-tyrosine and L-tryptophan.Therefore,in order to more clearly reveal the process of rumen bacterial regulation of MPY,we established the path of SEM based on the L-tyrosine,L-tryptophan and related components.The SEM based on the metabolites suggested that[Ruminococcus]gauvreauii group could inhibit the energy supply of serum tryptophan to MPY by milk S-lactoylglutathione,which could enhance pyruvate metabolism.Norank_f_Ruminococcaceae could increase the ruminal L-tyrosine,which could provide the substrate for MPY.Conclusion Our results indicated that the represented enterotype genera of Prevotella and Ruminococcus,and the hub genera of[Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae could regulate milk protein synthesis by affecting the ruminal L-tyrosine and L-tryptophan.Moreover,the combined analysis of enterotype,WGCNA and SEM could be used to connect rumen microbial metabolism with host metabolism,which provides a fundamental understanding of the crosstalk between host and microorganisms in regulating the synthesis of milk composition.展开更多
In 2011, the term ‘‘enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about...In 2011, the term ‘‘enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view.We firstly illustrated the definition of the enterotype and various factors influencing enterotypes,such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype analysis.Finally, we showed that the concept of enterotype has been extended to other ecological niches.Based on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.展开更多
To investigate the influence of baseline enterotypes and dietary starch type on the concentration of short-chain fatty acids(SCFA),numbers of butyrate producing bacteria and the expression of genes related to intestin...To investigate the influence of baseline enterotypes and dietary starch type on the concentration of short-chain fatty acids(SCFA),numbers of butyrate producing bacteria and the expression of genes related to intestinal barrier and inflammatory response in the colon of finishing pigs,a 60-d in vivo trial was conducted.A 2-wk pre-trial with 102 crossbred(Duroc×[Landrace×Yorkshire])finishing barrows(90 d old)was conducted to screen enterotypes.Then,a total of 32 pigs(87.40±2.76 kg)with high(HPBR,>14)and low(LPBR,<2)Prevotella-to-Bacteroides ratios(PBR)in equal measure were selected and randomly divided into 4 groups with 8 replicates per group and 1 pig per replicate.The trial was designed following a 2(PBR)×2(amylose-to-amylopectin ratio,AMR)factorial arrangement.Pigs with different PBR were fed diets based on corn-soybean meal with high AMR(HAMR,1.24)or low AMR(LAMR,0.23),respectively.Results showed that neither PBR nor AMR influenced the growth performance of pigs.HPBR pigs fed HAMR diet had a higher number of colonic Clostridium cluster XIVa and higher gene expression of butyrate kinase compared to the LPBR pigs(P<0.05).The HPBR pigs fed HAMR diets also had increased colonic concentrations of total SCFA and propionate compared to the LPBR pigs(P<0.05).Comparing with other pigs,HPBR pigs fed HAMR diets showed a lower(P<0.05)expression of histone deacetylases(HDAC)gene and higher(P<0.05)expression of G protein-coupled receptor 43 gene(GPR 43)in the colonic mucosa.The interaction(P<0.05)of HPBR and HAMR was also found to decrease the gene expression of interleukin(IL)-6,IL-12,IL-1βand tumor necrosis factor-α(TNF-α)in colonic mucosa.These findings show that HAMR diet increased the abundance and activity of butyrate-producing bacteria and the concentration and absorption of SCFA,which may be associated with the decreased gene expression of inflammatory cytokines in the colonic mucosa of pigs with Prevotella-rich enterotype.All these alterations are likely to have a positive effect on the intestinal health of finishing pigs.展开更多
BACKGROUND Recently, gut microbiota has been associated with various diseases other than intestinal disease. Thus, there has been rapid growth in the study of gut microbiota. Considering the numerous factors influenci...BACKGROUND Recently, gut microbiota has been associated with various diseases other than intestinal disease. Thus, there has been rapid growth in the study of gut microbiota. Considering the numerous factors influencing gut microbiota such as age, diet, etc., area-based research is required. Indonesia has numerous different tribes and each of these tribes have different lifestyles. Hence, it is expected that each tribe has a specific gut microbiota. A deeper insight into the composition of gut microbiota can be used to determine the condition of gut microbiota in Indonesians and to consider which treatment may be suitable and effective to improve health status.AIM To investigate the gut microbiota of Indonesian subjects represented by Javanese and Balinese tribes by analyzing fecal samples.METHODS Fecal samples were collected from a total of 80 individuals with 20 in each of the young groups ranging from 25-45 years and the elderly group aged 70 years or more from two different regions, Yogyakarta and Bali. Fecal sample collection was performed at the end of the assessment period(day 14 ± 1 d) during which time the subjects were not allowed to consume probiotic or antibiotic products.The quantification of various Clostridium subgroups, Lactobacillus subgroups,Enterococcus, Streptococcus, Staphylococcus, Bacteroides fragilis group and Prevotella,Bifidobacterium and Atopobium cluster, Enterobacteriaceae and Pseudomonas was performed using the Yakult intestinal flora-scan(YIF-SCAN).RESULTS The bacterial population in younger subjects' feces was higher than that in the elderly population, with a total of approximately 10.0 – 10.6 log10 bacterial cells/g feces. The most abundant bacteria in all groups were Clostridium, followed by Prevotella, Atopobium, Bifidobacterium and Bacteroides. In the elderly, an increase in Enterobacteriaceae, Coliform and Escherichia coli was found. In terms of bacterial counts in Yogyakarta, total bacteria, Clostridium coccoides(C. coccoides) group,Bifidobacterium, Prevotella, Lactobacillus plantarum subgroup, and Streptococcus were significantly higher(P < 0.05) in younger than elderly subjects, while the Lactobacillus gasseri subgroup, Lactobacillus casei subgroup, and Lactobacillus reuteri subgroup counts were significantly lower(P < 0.05) in younger subjects. In Balinese subjects, total bacteria, C. coccoides group, Clostridium leptum subgroup,Bacteroides fragilis group, and Prevotella were significantly higher(P < 0.05) in younger compared to elderly individuals, while the Lactobacillus ruminis subgroup, and Enterobacteriaceae were significantly lower(P < 0.05) in younger subjects. The results also revealed that, besides the C. coccoides group and Clostridium leptum group being the most abundant gut microbiota in both Yogyakarta and Balinese people, the latter was indicated by a higher Clostridium perfringens count, which was almost 10 times that of Yogyakarta subjects. This may be a response to different lifestyles in the different tribes; however, this phenomenon requires further extensive study.CONCLUSION Bacterial populations were higher in younger than in elderly subjects. Most abundant bacterial groups were Clostridium, Prevotella, Atopobium, Bifidobacterium,and Bacteroides. The level of Clostridium perfringens in Yogyakarta subjects was lower than that in Balinese subjects.展开更多
Intestinal dysbiosis is closely related to a variety of medical conditions,especially gastrointestinal diseases.The present study aimed to investigate the effects of koumiss on chronic atrophic gastritis(CAG)in an out...Intestinal dysbiosis is closely related to a variety of medical conditions,especially gastrointestinal diseases.The present study aimed to investigate the effects of koumiss on chronic atrophic gastritis(CAG)in an outpatient clinical trial(n=10;all female subjects aged 41-55;body mass index ranging from 19.5 to 25.8).Each patient consumed three servings of koumiss per day(i.e.250 ml daily before each of 3 meals)for a 60-day period.The improvement of patients'symptoms was monitored by comparing the total scores of symptoms before and after the treatment.Meanwhile,the changes in the patients’fecal microbiota composition and specific blood parameters were determined.After the 60-day koumiss administration,significant symptom improvements were observed,as evidenced by the reduction of the total symptoms score,and changes in blood platelet and cholesterol levels.The changes in patients’fecal microbiota composition were found.The patients’fecal microbiota fell into two distinct enterotypes,Bacteroides dorei/Bacteroides uniformis(BB-enterotype)and Prevotella copri(P-enterotype).Significant less Bacteroides uniformis was found in the BB-enterotype patient group,while significant more butyrate-producing bacteria(e.g.Eubacterium rectale and Faecalibacterium prausnitzii)were found in the P-enterotype patient group,following koumiss administration.After stopping koumiss consumption,the relative abundance of some biomarker taxa returned to the original level,suggesting that the gut microbiota modulatory effect was not permanent and that continuous koumiss administration was required to maintain the therapeutic effect.In conclusion,koumiss consumption could alleviate the symptoms of CAG patients.Our results may help understand the mechanism of koumiss in alleviating CAG disease symptoms,facilitating the development of such products with desired therapeutic functions.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
The gut microbiota of intensive care unit(ICU)patients displays extreme dysbiosis associated with increased susceptibility to organ failure,sepsis,and septic shock.However,such dysbiosis is difficult to characterize o...The gut microbiota of intensive care unit(ICU)patients displays extreme dysbiosis associated with increased susceptibility to organ failure,sepsis,and septic shock.However,such dysbiosis is difficult to characterize owing to the high dimensional complexity of the gut microbiota.We tested whether the concept of enterotype can be applied to the gut microbiota of ICU patients to describe the dysbiosis.We collected 131 fecal samples from 64 ICU patients diagnosed with sepsis or septic shock and performed 16S rRNA gene sequencing to dissect their gut microbiota compositions.During the development of sepsis or septic shock and during various medical treatments,the ICU patients always exhibited two dysbiotic microbiota patterns,or ICU-enterotypes,which could not be explained by host properties such as age,sex,and body mass index,or external stressors such as infection site and antibiotic use.ICU-enterotype I(ICU E1)comprised predominantly Bacteroides and an unclassified genus of Enterobacteriaceae,while ICU-enterotype II(ICU E2)comprised predominantly Enterococcus.Among more critically ill patients with Acute Physiology and Chronic Health Evaluation II(APACHE II)scores>18,septic shock was more likely to occur with ICU E1(P=0.041).Additionally,ICU E1 was correlated with high serum lactate levels(P=0.007).Therefore,different patterns of dysbiosis were correlated with different clinical outcomes,suggesting that ICU-enterotypes should be diagnosed as independent clinical indices.Thus,the microbial-based human index classifier we propose is precise and effective for timely monitoring of ICU-enterotypes of individual patients.This work is a first step toward precision medicine for septic patients based on their gut microbiota profiles.展开更多
Fecal microbiota transplantation(FMT)of human fecal samples into germ-free(GF)mice is useful for establishing causal relationships between the gut microbiota and human phenotypes.However,due to the intrinsic differenc...Fecal microbiota transplantation(FMT)of human fecal samples into germ-free(GF)mice is useful for establishing causal relationships between the gut microbiota and human phenotypes.However,due to the intrinsic differences between human and mouse intestines and the different diets of the two organisms,it may not be possible to replicate human phenotypes in mice through FMT;similarly,treatments that are effective in mouse models may not be effective in humans.In this study,we aimed to identify human gut microbes that undergo significant and consistent changes(i.e.,in relative abundances)after transplantation into GF mice in multiple experimental settings.We collected 16S rDNA-seq data from four published studies and analyzed the gut microbiota profiles from 1713 human–mouse pairs.Strikingly,on average,we found that only 47%of the human gut microbes could be re-established in mice at the species level,among which more than 1/3 underwent significant changes(referred to as“variable taxa”).Most of the human gut microbes that underwent significant changes were consistent across multiple human–mouse pairs and experimental settings.Consequently,about 1/3 of human samples changed their enterotypes,i.e.,significant changes in their leading species after FMT.Mice fed with a controlled diet showed a lower enterotype change rate(23.5%)than those fed with a noncontrolled diet(49.0%),suggesting a possible solution for rescue.Most of the variable taxa have been reported to be implicated in human diseases,with some recognized as the causative species.Our results highlight the challenges of using a mouse model to replicate human gut microbiota-associated phenotypes,provide useful information for researchers using mice in gut microbiota studies,and call for additional validations after FMT.An online database named FMT-DB is publicly available at http://fmt2mice.humangut.info/#/.展开更多
基金supported by the National Natural Science Foundation of China(Nos.82101665,82271588,82200665,and 82100795)the Zhejiang Provincial Natural Science Foundation of China(No.LY22H030009)+1 种基金the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine(No.2023ZL480)the Medical and Health Research Project of Zhejiang Province(No.2023RC153),China.
文摘Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging,yet there is limited understanding of gut microbiome variation in advanced age.Here,we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years,with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations.In addition to two adult-like enterotypes dominated by Bacteroides(ET-Bacteroides)and Prevotella(ET-Prevotella),we identified a novel enterotype dominated by Escherichia(ET-Escherichia),whose prevalence increased in advanced age.Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus(T2DM)or diet.We characterized the distinct taxonomic and functional profiles of ET-Escherichia,and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype,as well as the lowest species diversity.In addition,we carried out a series of correlation analyses and co-abundance network analyses,which showed that several factors were likely linked to the overabundance of Escherichia members,including advanced age,vegetable intake,and fruit intake.Overall,our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population.Considering the different age distribution of each enterotype,these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.
基金the National Natural Science Foundation of China(32272829,32072761,31902184)Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project(20220203).
文摘Background Dairy cows’lactation performance is the outcome of the crosstalk between ruminal microbial metabo-lism and host metabolism.However,it is still unclear to what extent the rumen microbiome and its metabolites,as well as the host metabolism,contribute to regulating the milk protein yield(MPY).Methods The rumen fluid,serum and milk of 12 Holstein cows with the same diet(45%coarseness ratio),parity(2–3 fetuses)and lactation days(120–150 d)were used for the microbiome and metabolome analysis.Rumen metabolism(rumen metabolome)and host metabolism(blood and milk metabolome)were connected using a weighted gene co-expression network(WGCNA)and the structural equation model(SEM)analyses.Results Two different ruminal enterotypes,with abundant Prevotella and Ruminococcus,were identified as type1 and type2.Of these,a higher MPY was found in cows with ruminal type2.Interestingly,[Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae(the differential bacteria)were the hub genera of the network.In addition,differential ruminal,serum and milk metabolome between enterotypes were identified,where the cows with type2 had higher L-tyrosine of rumen,ornithine and L-tryptophan of serum,and tetrahydroneopterin,palmitoyl-L-carnitine,S-lactoylglutathione of milk,which could provide more energy and substrate for MPY.Further,based on the identi-fied modules of ruminal microbiome,as well as ruminal serum and milk metabolome using WGCNA,the SEM analysis indicated that the key ruminal microbial module1,which contains the hub genera of the network([Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae)and high abundance of bacteria(Prevotella and Ruminococcus),could regulate the MPY by module7 of rumen,module2 of blood,and module7 of milk,which contained L-tyrosine and L-tryptophan.Therefore,in order to more clearly reveal the process of rumen bacterial regulation of MPY,we established the path of SEM based on the L-tyrosine,L-tryptophan and related components.The SEM based on the metabolites suggested that[Ruminococcus]gauvreauii group could inhibit the energy supply of serum tryptophan to MPY by milk S-lactoylglutathione,which could enhance pyruvate metabolism.Norank_f_Ruminococcaceae could increase the ruminal L-tyrosine,which could provide the substrate for MPY.Conclusion Our results indicated that the represented enterotype genera of Prevotella and Ruminococcus,and the hub genera of[Ruminococcus]gauvreauii group and norank_f_Ruminococcaceae could regulate milk protein synthesis by affecting the ruminal L-tyrosine and L-tryptophan.Moreover,the combined analysis of enterotype,WGCNA and SEM could be used to connect rumen microbial metabolism with host metabolism,which provides a fundamental understanding of the crosstalk between host and microorganisms in regulating the synthesis of milk composition.
基金supported by the National Key R&D Program of China (Grant No. 2018YFC0910502)the National Natural Science Foundation of China (Grant Nos. 61103167, 31271410, and 31671374)
文摘In 2011, the term ‘‘enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view.We firstly illustrated the definition of the enterotype and various factors influencing enterotypes,such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype analysis.Finally, we showed that the concept of enterotype has been extended to other ecological niches.Based on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.
基金The National Natural Science Foundation of China(NSFC,grant number 31730091,31872369 and 31672436).
文摘To investigate the influence of baseline enterotypes and dietary starch type on the concentration of short-chain fatty acids(SCFA),numbers of butyrate producing bacteria and the expression of genes related to intestinal barrier and inflammatory response in the colon of finishing pigs,a 60-d in vivo trial was conducted.A 2-wk pre-trial with 102 crossbred(Duroc×[Landrace×Yorkshire])finishing barrows(90 d old)was conducted to screen enterotypes.Then,a total of 32 pigs(87.40±2.76 kg)with high(HPBR,>14)and low(LPBR,<2)Prevotella-to-Bacteroides ratios(PBR)in equal measure were selected and randomly divided into 4 groups with 8 replicates per group and 1 pig per replicate.The trial was designed following a 2(PBR)×2(amylose-to-amylopectin ratio,AMR)factorial arrangement.Pigs with different PBR were fed diets based on corn-soybean meal with high AMR(HAMR,1.24)or low AMR(LAMR,0.23),respectively.Results showed that neither PBR nor AMR influenced the growth performance of pigs.HPBR pigs fed HAMR diet had a higher number of colonic Clostridium cluster XIVa and higher gene expression of butyrate kinase compared to the LPBR pigs(P<0.05).The HPBR pigs fed HAMR diets also had increased colonic concentrations of total SCFA and propionate compared to the LPBR pigs(P<0.05).Comparing with other pigs,HPBR pigs fed HAMR diets showed a lower(P<0.05)expression of histone deacetylases(HDAC)gene and higher(P<0.05)expression of G protein-coupled receptor 43 gene(GPR 43)in the colonic mucosa.The interaction(P<0.05)of HPBR and HAMR was also found to decrease the gene expression of interleukin(IL)-6,IL-12,IL-1βand tumor necrosis factor-α(TNF-α)in colonic mucosa.These findings show that HAMR diet increased the abundance and activity of butyrate-producing bacteria and the concentration and absorption of SCFA,which may be associated with the decreased gene expression of inflammatory cytokines in the colonic mucosa of pigs with Prevotella-rich enterotype.All these alterations are likely to have a positive effect on the intestinal health of finishing pigs.
文摘BACKGROUND Recently, gut microbiota has been associated with various diseases other than intestinal disease. Thus, there has been rapid growth in the study of gut microbiota. Considering the numerous factors influencing gut microbiota such as age, diet, etc., area-based research is required. Indonesia has numerous different tribes and each of these tribes have different lifestyles. Hence, it is expected that each tribe has a specific gut microbiota. A deeper insight into the composition of gut microbiota can be used to determine the condition of gut microbiota in Indonesians and to consider which treatment may be suitable and effective to improve health status.AIM To investigate the gut microbiota of Indonesian subjects represented by Javanese and Balinese tribes by analyzing fecal samples.METHODS Fecal samples were collected from a total of 80 individuals with 20 in each of the young groups ranging from 25-45 years and the elderly group aged 70 years or more from two different regions, Yogyakarta and Bali. Fecal sample collection was performed at the end of the assessment period(day 14 ± 1 d) during which time the subjects were not allowed to consume probiotic or antibiotic products.The quantification of various Clostridium subgroups, Lactobacillus subgroups,Enterococcus, Streptococcus, Staphylococcus, Bacteroides fragilis group and Prevotella,Bifidobacterium and Atopobium cluster, Enterobacteriaceae and Pseudomonas was performed using the Yakult intestinal flora-scan(YIF-SCAN).RESULTS The bacterial population in younger subjects' feces was higher than that in the elderly population, with a total of approximately 10.0 – 10.6 log10 bacterial cells/g feces. The most abundant bacteria in all groups were Clostridium, followed by Prevotella, Atopobium, Bifidobacterium and Bacteroides. In the elderly, an increase in Enterobacteriaceae, Coliform and Escherichia coli was found. In terms of bacterial counts in Yogyakarta, total bacteria, Clostridium coccoides(C. coccoides) group,Bifidobacterium, Prevotella, Lactobacillus plantarum subgroup, and Streptococcus were significantly higher(P < 0.05) in younger than elderly subjects, while the Lactobacillus gasseri subgroup, Lactobacillus casei subgroup, and Lactobacillus reuteri subgroup counts were significantly lower(P < 0.05) in younger subjects. In Balinese subjects, total bacteria, C. coccoides group, Clostridium leptum subgroup,Bacteroides fragilis group, and Prevotella were significantly higher(P < 0.05) in younger compared to elderly individuals, while the Lactobacillus ruminis subgroup, and Enterobacteriaceae were significantly lower(P < 0.05) in younger subjects. The results also revealed that, besides the C. coccoides group and Clostridium leptum group being the most abundant gut microbiota in both Yogyakarta and Balinese people, the latter was indicated by a higher Clostridium perfringens count, which was almost 10 times that of Yogyakarta subjects. This may be a response to different lifestyles in the different tribes; however, this phenomenon requires further extensive study.CONCLUSION Bacterial populations were higher in younger than in elderly subjects. Most abundant bacterial groups were Clostridium, Prevotella, Atopobium, Bifidobacterium,and Bacteroides. The level of Clostridium perfringens in Yogyakarta subjects was lower than that in Balinese subjects.
文摘Intestinal dysbiosis is closely related to a variety of medical conditions,especially gastrointestinal diseases.The present study aimed to investigate the effects of koumiss on chronic atrophic gastritis(CAG)in an outpatient clinical trial(n=10;all female subjects aged 41-55;body mass index ranging from 19.5 to 25.8).Each patient consumed three servings of koumiss per day(i.e.250 ml daily before each of 3 meals)for a 60-day period.The improvement of patients'symptoms was monitored by comparing the total scores of symptoms before and after the treatment.Meanwhile,the changes in the patients’fecal microbiota composition and specific blood parameters were determined.After the 60-day koumiss administration,significant symptom improvements were observed,as evidenced by the reduction of the total symptoms score,and changes in blood platelet and cholesterol levels.The changes in patients’fecal microbiota composition were found.The patients’fecal microbiota fell into two distinct enterotypes,Bacteroides dorei/Bacteroides uniformis(BB-enterotype)and Prevotella copri(P-enterotype).Significant less Bacteroides uniformis was found in the BB-enterotype patient group,while significant more butyrate-producing bacteria(e.g.Eubacterium rectale and Faecalibacterium prausnitzii)were found in the P-enterotype patient group,following koumiss administration.After stopping koumiss consumption,the relative abundance of some biomarker taxa returned to the original level,suggesting that the gut microbiota modulatory effect was not permanent and that continuous koumiss administration was required to maintain the therapeutic effect.In conclusion,koumiss consumption could alleviate the symptoms of CAG patients.Our results may help understand the mechanism of koumiss in alleviating CAG disease symptoms,facilitating the development of such products with desired therapeutic functions.
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This work was partially supported by special Fund for Clinical Research of Wu Jieping Medical Foundation,China(Grant No.320.6750.18422)the Ministry of Science and Technology of the People’s Republic of China(Grant No.2018YFC0910502)the National Natural Science Foundation of China(Grant Nos.31871334 and 31671374).
文摘The gut microbiota of intensive care unit(ICU)patients displays extreme dysbiosis associated with increased susceptibility to organ failure,sepsis,and septic shock.However,such dysbiosis is difficult to characterize owing to the high dimensional complexity of the gut microbiota.We tested whether the concept of enterotype can be applied to the gut microbiota of ICU patients to describe the dysbiosis.We collected 131 fecal samples from 64 ICU patients diagnosed with sepsis or septic shock and performed 16S rRNA gene sequencing to dissect their gut microbiota compositions.During the development of sepsis or septic shock and during various medical treatments,the ICU patients always exhibited two dysbiotic microbiota patterns,or ICU-enterotypes,which could not be explained by host properties such as age,sex,and body mass index,or external stressors such as infection site and antibiotic use.ICU-enterotype I(ICU E1)comprised predominantly Bacteroides and an unclassified genus of Enterobacteriaceae,while ICU-enterotype II(ICU E2)comprised predominantly Enterococcus.Among more critically ill patients with Acute Physiology and Chronic Health Evaluation II(APACHE II)scores>18,septic shock was more likely to occur with ICU E1(P=0.041).Additionally,ICU E1 was correlated with high serum lactate levels(P=0.007).Therefore,different patterns of dysbiosis were correlated with different clinical outcomes,suggesting that ICU-enterotypes should be diagnosed as independent clinical indices.Thus,the microbial-based human index classifier we propose is precise and effective for timely monitoring of ICU-enterotypes of individual patients.This work is a first step toward precision medicine for septic patients based on their gut microbiota profiles.
基金supported by the National Key R&D Program of China(Grant Nos.2018YFC0910502 and 2018YFC0910500 to WHC)the National Natural Science Foundation of China(Grant Nos.61932008,61772368,and 61572363)+1 种基金the Natural Science Foundation of Shanghai,China(Grant No.17ZR1445600)the Shanghai Municipal Science and Technology Major Project,China(Grant No.2018SHZDZX01).
文摘Fecal microbiota transplantation(FMT)of human fecal samples into germ-free(GF)mice is useful for establishing causal relationships between the gut microbiota and human phenotypes.However,due to the intrinsic differences between human and mouse intestines and the different diets of the two organisms,it may not be possible to replicate human phenotypes in mice through FMT;similarly,treatments that are effective in mouse models may not be effective in humans.In this study,we aimed to identify human gut microbes that undergo significant and consistent changes(i.e.,in relative abundances)after transplantation into GF mice in multiple experimental settings.We collected 16S rDNA-seq data from four published studies and analyzed the gut microbiota profiles from 1713 human–mouse pairs.Strikingly,on average,we found that only 47%of the human gut microbes could be re-established in mice at the species level,among which more than 1/3 underwent significant changes(referred to as“variable taxa”).Most of the human gut microbes that underwent significant changes were consistent across multiple human–mouse pairs and experimental settings.Consequently,about 1/3 of human samples changed their enterotypes,i.e.,significant changes in their leading species after FMT.Mice fed with a controlled diet showed a lower enterotype change rate(23.5%)than those fed with a noncontrolled diet(49.0%),suggesting a possible solution for rescue.Most of the variable taxa have been reported to be implicated in human diseases,with some recognized as the causative species.Our results highlight the challenges of using a mouse model to replicate human gut microbiota-associated phenotypes,provide useful information for researchers using mice in gut microbiota studies,and call for additional validations after FMT.An online database named FMT-DB is publicly available at http://fmt2mice.humangut.info/#/.
