Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon

One carbon (1C) metabolism nutrients influence epigenetic regulation and they are supplied by diet and synthesized by gut microbiota. We examined the association between dietary consumption of methyl donors (methionine, betaine and choline) and B vitamins (folate, B2, B6, and B12) and the community composition and structure of the colonic mucosa-associated gut microbiota determined by 16S rRNA gene sequencing in 97 colonic biopsies of 35 men. We used the food frequency questionnaire to assess daily consumption of nutrients, and the UPARSE and SILVA databases for operational taxonomic unit classification. The difference in bacterial diversity and taxonomic relative abundance were compared between low versus high consumption of these nutrients. False discover rate (FDR) adjusted p value < 0.05 indicated statistical significance. The bacterial richness and composition differed significantly by the consumption of folate and B vitamins (p < 0.001). Compared with higher consumption, a lower consumption of these nutrients was associated with a lower abundance of Akkermansia (folate), Roseburia (vitamin B2), and Faecalibacterium (vitamins B2, B6, and B12) but a higher abundance of Erysipelatoclostridium (vitamin B2) (FDR p values < 0.05). The community composition and structure of the colonic bacteria differed significantly by dietary consumption of folate and B vitamins.

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Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

Journal of Personalized Medicine ◽

10.3390/jpm11040294 ◽

2021 ◽

Vol 11 (4) ◽

pp. 294

Author(s):

Irina Grigor’eva ◽

Tatiana Romanova ◽

Natalia Naumova ◽

Tatiana Alikina ◽

Alexey Kuznetsov ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Gallstone Disease ◽

Illumina Miseq ◽

Rrna Gene ◽

Bacterial Phyla ◽

Female Patients ◽

Composition And Structure ◽

Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

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Changes in rearing conditions rapidly modify gut microbiota structure in Tenebrio molitor larvae

10.1101/423178 ◽

2018 ◽

Cited By ~ 1

Author(s):

Marine Cambon ◽

Jean-Claude Ogier ◽

Anne Lanois ◽

Jean-Baptiste Ferdy ◽

Sophie Gaudriault

Keyword(s):

Gut Microbiota ◽

Housekeeping Gene ◽

Tenebrio Molitor ◽

Absolute Quantification ◽

Rrna Gene ◽

Composition And Structure ◽

Rearing Conditions ◽

Mutualistic Relationship ◽

Taxonomic Groups ◽

Multicellular Organisms

AbstractThe gut microbiota of multicellular organisms has been shown to play a key role in their host biology. In mammals, it has an invariant component, responsible for establishing a mutualistic relationship with the host. It also contains a dynamic fraction which facilitates adaptation in response to changes in the environment. These features have been well described in mammals, but little is known about microbiota stability or plasticity in insects. We assessed changes in microbiota composition and structure in a reared insect after a change in rearing conditions. We reared Tenebrio molitor (Coleoptera, Tenebrioninae) larvae for five days in soil samples from two river banks and analyzed their gut microbial communities by a metabarcoding technique, using the V3-V4 region of the 16S rRNA gene and the housekeeping gene gyrB. We found that soil-reared insects had a significantly more diverse microbiota than the control insects and that insects reared in soil from different sites had significantly different microbiota. We confirmed this trend by absolute quantification of the two mains fluctuating taxonomic groups: the Enterobacteriaceae family and the Pseudomonas genus, dominant in the soil-reared insects and in the control insects, respectively. Our results suggest the existence of a resident microbiota in T. molitor gut, but indicate that rearing changes can induce rapid and profound changes in the relative abundance of some of the members of this resident microbiota.

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B7 Family Molecule VSIG4 Regulates Intestinal Anti-Enterohemorrhagic Escherichia coli Immunity by Altering Gut Flora Diversity

Microorganisms ◽

10.3390/microorganisms9081769 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1769

Author(s):

Zhili He ◽

Jiajia Li ◽

Saisai Gong ◽

Li Xing ◽

Yakun Sun ◽

...

Keyword(s):

Escherichia Coli ◽

Gut Microbiota ◽

Community Composition ◽

Average Length ◽

Enterohemorrhagic Escherichia Coli ◽

Rrna Gene ◽

B7 Family ◽

Immunoglobulin Domain ◽

Flora Diversity

As an essential member of the B7 family, V-set and immunoglobulin domain-containing 4 (VSIG4) is expressed explicitly in tissue-resident macrophages (TRMs) and plays an essential role in maintaining the homeostasis of the environmental immune system. Here, we demonstrate that gene-targeted VSIG4-deficient mice infected with Enterohemorrhagic Escherichia coli (EHEC) display reduced bacterial burden. To reveal the role of VSIG4 in the fight against EHEC infection, we collected mice feces and used high-throughput 16S rRNA gene amplicons to detect changes in the flora. A total of 657330 sequences were sequenced on the PacBio platform, with an average length of 1498 bp. We found that VSIG4 deficiency could alter the gut microbiota by increasing diversity and shifting community composition. In particular, G_Akkermansia and G_Oscillo spiraceae increased significantly. These findings expand upon a prior observation that VSIG4 deficiency reduced EHEC colonization by changing the gut microbiota diversity and shifting community composition.

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196 Direct comparison of human microbiota-associated (HMA) gnotobiotic piglet and mouse models

Journal of Animal Science ◽

10.1093/jas/skz122.203 ◽

2019 ◽

Vol 97 (Supplement_2) ◽

pp. 114-115

Author(s):

Nirosh D Aluthge ◽

Wesley A Tom ◽

Alison C Bartenslager ◽

Thomas E Burkey ◽

Kelly D Heath ◽

...

Keyword(s):

Animal Models ◽

Gut Microbiota ◽

Bacterial Communities ◽

Statistical Significance ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Human Donor ◽

Fecal Samples ◽

Human Microbiota ◽

Nutritional Studies

Abstract The objective of this study was to compare the establishment of human fecal bacterial communities in porcine and murine animal models. Many gut microbiota studies use human microbiota-associated (HMA) rodents as translational animal models; however, it has been questioned as to how successfully a human microbiota can be established in rodents considering the many differences that exist between rodents and humans. The domestic pig (Sus scrofa domesticus) has many anatomical, physiological, and immunological similarities to humans and has been widely used as a model for humans in biomedical and nutritional studies. Thus, the porcine model may be an alternative to rodent models in gut microbiota research. The current study was designed to evaluate the establishment of the same human donor microbiota in the rodent and pig models. Both germ-free piglets and mice (C3H/HeN) were transplanted with fecal microbiota from four human donors: Infant (0–5 m), child (1–12 yrs), adult (18–64 yrs), and elderly (65+ yrs). To monitor the establishment of the transplanted microbiota, weekly fecal samples were collected for 5 wks. All fecal samples were subjected to 16S rRNA gene-based amplicon sequencing using the Illumina MiSeqTM platform to characterize bacterial community composition. Unweighted unifrac distances were compared between the bacterial communities of the human donor and the corresponding HMA porcine and murine fecal samples. Statistical significance was tested using the Mann-Whitney U test (P = 0.05). This analysis suggested that more taxa are colonized in the mice compared to the piglets receiving the same infant donor microbiota, while for the child, adult, and elderly donors, the piglet model established the human donor microbiota better than the mice receiving the same donor samples. This suggests that in the latter stages of human development, more species of the human fecal inoculum colonizes the pig gut compared to the mouse gut.

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Seasonal Breeding Leads to Changes for Gut Microbiota Diversity in the Wild Ground Squirrel (Spermophilus Dauricus)

10.21203/rs.3.rs-96089/v1 ◽

2020 ◽

Author(s):

Xiaoying Yang ◽

Yuchen Yao ◽

Xueying Zhang ◽

Jiahui Zhong ◽

Fuli Gao ◽

...

Keyword(s):

Gut Microbiota ◽

Community Composition ◽

Breeding Season ◽

Ground Squirrel ◽

Microbial Community Composition ◽

16S Rrna Gene Sequencing ◽

Nucleotide Metabolism ◽

Rrna Gene ◽

Seasonal Breeding ◽

In The Wild

Abstract Background: Seasonal breeding is a normal phenomenon that animals adapt to natural selection and reproduce only in specific seasons. With the gradual popularization of Next-generation sequencing (NGS), large studies have shown that seasonal breeding has been affected by gut microbiota. Consequently, the purpose of this study is to explore the effect of seasonal breeding on the gut microbiota of wild ground squirrel (Spermophilus dauricus). We used 16S rRNA gene sequencing technology to sequence the gut microbiota of the wild ground squirrel in the breeding season and non-breeding season. We also predicted the function of gut microbiota by bioinformatic software.Results: The results showed that the main components of gut microbiota in all samples consisted of Firmicutes (61.8%), Bacteroidetes (32.4%), and Proteobacteria (3.7%). Microbial community composition analyses revealed significant differences between these two groups. At the genus level, Alistipes, Mycoplasma, Anaerotruncus, and Odoribacter were up-regulated in the non-breeding season, while Blautia and Streptococcus spp. were up-regulated in the breeding season. The result of function prediction suggested that the relative abundance of functional categories related to lipid metabolism, carbohydrate metabolism, and nucleotide metabolism was higher in the breeding season. The expression of transcription, energy metabolism, and signal transduction was enriched in the non-breeding season. Conclusions: Overall, the results of this study emphasized the significant effects of seasonal breeding on gut microbiota community composition of the wild ground squirrel and laid a foundation for further study of gut microbiota on seasonal breeding in the future.

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Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock

Scientific Reports ◽

10.1038/s41598-021-85897-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sandra A. Appiah ◽

Christine L. Foxx ◽

Dominik Langgartner ◽

Annette Palmer ◽

Cristian A. Zambrano ◽

...

Keyword(s):

Gut Microbiota ◽

Community Composition ◽

Gut Microbiome ◽

Beta Diversity ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Global Changes ◽

Rrna Gene ◽

Alpha And Beta Diversity ◽

Increased Risk

AbstractSevere injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.

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Comparative Analysis of Fecal Bacterial Microbiota of Six Bird Species

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.791287 ◽

2021 ◽

Vol 8 ◽

Author(s):

Li Gao ◽

Li Liu ◽

Chao Du ◽

Qiangchuan Hou

Keyword(s):

Gut Microbiota ◽

Community Composition ◽

Bacterial Species ◽

Bird Species ◽

Living Environment ◽

Rrna Gene ◽

Muscovy Duck ◽

Microbial Composition ◽

Gut Microbes ◽

Whooper Swan

The gut microbiota contributes to host health by maintaining homeostasis and improving digestive efficiency. Therefore, identifying gut microbes will shed light on the annual life cycle of animals and in particular those that are threatened or endangered. Nonetheless, the gut microbial composition of the majority of bird species is still unknown. Here, for the first time, 16S rRNA gene sequencing was used to characterize and compare the community composition and diversity of gut microbiotas from six species of birds raised at the Wildlife Conservation Center in Baotou, China: relict gull (Larus relictus; n = 3), muscovy duck (Cairina moschata; n = 3), ruddy shelduck (Tadorna ferruginea; n = 3), demoiselle crane (Anthropoides virgo; n = 4), whooper swan (Cygnus cygnus; n = 3), and black swan (Cygnus atratus; n = 5). A total of 26,616 operational taxonomic units from 21 samples were classified into 32 phyla and 507 genera. Chao1, Shannon diversity, observed species, and Simpson index analysis revealed differences in the community richness and diversity between the different species. Proteobacteria was the dominant bacterial phylum in whooper swan and relict gull, whereas Firmicutes was the dominant bacterial phylum in the other species. At the genus level, 11 dominant genera were detected (Lactobacillus, Psychrobacter, Enterococcus, Carnobacterium, Weissella, Burkholderia, Escherichia/Shigella, Leuconostoc, Buttiauxella, Desemzia, and Staphylococcus). Principal component and cluster analyses revealed that, while the microbial community composition of different individuals of the same species clustered together, the gut microbial composition varied between the bird species. Furthermore, the most abundant bacterial species differed between bird species. Because many avian gut microbes are derived from the diet, the eating habits and natural living environment of birds may be important contributing factors to the observed differences. Short-term changes to the diet and living environment have little effect on the composition of the avian gut microbiota. This study provides a theoretical basis for bird protection, including disease prevention and control.

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Effects of Clostridium butyricum on growth performance, metabonomics and intestinal microbial differences of weaned piglets

BMC Microbiology ◽

10.1186/s12866-021-02143-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jing Liang ◽

Shasha Kou ◽

Cheng Chen ◽

Sayed Haidar Abbas Raza ◽

Sihu Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Growth Performance ◽

Intestinal Microbiota ◽

Relative Abundance ◽

Statistical Significance ◽

Clostridium Butyricum ◽

Rrna Gene ◽

Gut Health ◽

Weaned Piglets ◽

Bacterial Phyla

Abstract Background Weaning stress of piglets causes a huge economic loss to the pig industry. Balance and stability of the intestinal microenvironment is an effective way to reduce the occurance of stress during the weaning process. Clostridium butyricum, as a new microecological preparation, is resistant to high temperature, acid, bile salts and some antibiotics. The aim of present study is to investigate the effects of C. butyricum on the intestinal microbiota and their metabolites in weaned piglets. Results There was no statistical significance in the growth performance and the incidence of diarrhoea among the weaned piglets treated with C. butyricum during 0–21 days experimental period. Analysis of 16S rRNA gene sequencing results showed that the operational taxonomic units (OTUs), abundance-based coverage estimator (ACE) and Chao index of the CB group were found to be significantly increased compared with the NC group (P < 0.05). Bacteroidetes, Firmicutes and Tenericutes were the predominant bacterial phyla in the weaned piglets. A marked increase in the relative abundance of Megasphaera, Ruminococcaceae_NK4A214_group and Prevotellaceae_UCG-003, along with a decreased relative abundance of Ruminococcaceae_UCG-005 was observed in the CB group, when compared with the NC group (P < 0.05). With the addition of C. butyricum, a total of twenty-two significantly altered metabolites were obtained in the feces of piglets. The integrated pathway analysis by MetaboAnalyst indicated that arginine and proline metabolism; valine, leucine and isoleucine biosynthesis; and phenylalanine metabolism were the main three altered pathways, based on the topology. Furthermore, Spearman’s analysis revealed some altered gut microbiota genus such as Oscillospira, Ruminococcaceae_NK4A214_group, Megasphaera, Ruminococcaceae_UCG-005, Prevotella_2, Ruminococcaceae_UCG-002, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-003 were associated with the alterations in the fecal metabolites (P < 0.05), indicating that C. butyricum presented a potential protective impact through gut microbiota. The intestinal metabolites changed by C. butyricum mainly involved the variation of citrulline, dicarboxylic acids, branched-chain amino acid and tryptophan metabolic pathways. Conclusions Overall, this study strengthens the idea that the dietary C. butyricum treatment can significantly alter the intestinal microbiota and metabolite profiles of the weaned piglets, and C. butyricum can offer potential benefits for the gut health.

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Meta-analysis To Define a Core Microbiota in the Swine Gut

mSystems ◽

10.1128/msystems.00004-17 ◽

2017 ◽

Vol 2 (3) ◽

Cited By ~ 81

Author(s):

Devin B. Holman ◽

Brian W. Brunelle ◽

Julian Trachsel ◽

Heather K. Allen

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Meta Analysis ◽

Country Of Origin ◽

Rrna Gene ◽

Gi Tract ◽

Potential Health ◽

Core Microbiota ◽

Composition And Structure

ABSTRACT The results of this meta-analysis demonstrate that “study” and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age, or breed. Thus, these results provide the framework for future studies to manipulate the swine gut microbiota for potential health benefits. The swine gut microbiota encompasses a large and diverse population of bacteria that play a significant role in pig health. As such, a number of recent studies have utilized high-throughput sequencing of the 16S rRNA gene to characterize the composition and structure of the swine gut microbiota, often in response to dietary feed additives. It is important to determine which factors shape the composition of the gut microbiota among multiple studies and if certain bacteria are always present in the gut microbiota of swine, independently of study variables such as country of origin and experimental design. Therefore, we performed a meta-analysis using 20 publically available data sets from high-throughput 16S rRNA gene sequence studies of the swine gut microbiota. Next to the “study” itself, the gastrointestinal (GI) tract section that was sampled had the greatest effect on the composition and structure of the swine gut microbiota (P = 0.0001). Technical variation among studies, particularly the 16S rRNA gene hypervariable region sequenced, also significantly affected the composition of the swine gut microbiota (P = 0.0001). Despite this, numerous commonalities were discovered. Among fecal samples, the genera Prevotella, Clostridium, Alloprevotella, and Ruminococcus and the RC9 gut group were found in 99% of all fecal samples. Additionally, Clostridium, Blautia, Lactobacillus, Prevotella, Ruminococcus, Roseburia, the RC9 gut group, and Subdoligranulum were shared by >90% of all GI samples, suggesting a so-called “core” microbiota for commercial swine worldwide. IMPORTANCE The results of this meta-analysis demonstrate that “study” and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age, or breed. Thus, these results provide the framework for future studies to manipulate the swine gut microbiota for potential health benefits.

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Colonic Mucosa-associated Mycobiota in Individuals With Normal Colons

10.21203/rs.3.rs-1147234/v1 ◽

2021 ◽

Author(s):

Themistoklis Kourkoumpetis ◽

Kristi L. Hoffman ◽

Yuna Kim ◽

David Y. Graham ◽

Donna L. White ◽

...

Keyword(s):

Community Composition ◽

Large Intestine ◽

Relative Abundance ◽

Beta Diversity ◽

Colonic Mucosa ◽

Alpha Diversity ◽

Common Species ◽

Rrna Gene ◽

Fungal Community Composition ◽

Colon And Rectum

Abstract To characterize the spatial variation of the mucosa-associated adherent mycobiota along the large intestine in individuals with a normal-colon, we performed eukaryotic rRNA operon’s internal transcribed spacer-2 sequencing to profile fungal community composition and structure in 70 mucosal biopsies taken from the cecum, ascending, transverse, descending colon, and rectum of 14 polyp-free individuals. The bacteriome of these samples was previously characterized by sequencing the V4 region of the 16S rRNA gene. We identified 64 amplicon sequence variants (ASVs) with the relative abundance no less than 0.05% from these colonic mucosa samples. Each individual has a unique community composition of the gut mycobiome (P = 0.001 for beta diversity). Alpha-diversity and beta-diversity did not differ significantly across the colon segments. The most common phyla (relative abundance) were Ascomycota (45.4%) and Basidiomycota (45.3%). The most common genera were Malassezia (28.2%) and Candida (13.4%). Malassezia was found in 13 of 14 individuals. Other fungi genera were sporadically found in the large intestine. The most common species were Malassezia restricta (22.7%), Candida albicans (11.9%), Malasseziales sp. (8.80%), unclassified fungi (7.80%), and Penicillium paneum (5.70%). Malasseziaceae was co-abundant with Enterobacteriaceae and co-exclusive with Barnesiellaceae, Rikenellaceae, and Acidaminococcaceae. Malassezia was widely colonized whereas other fungal genera were sporadically colonized in the large intestine. The physiologic and pathogenic functions of fungi in human gastrointestinal tract including Malasseziaceae that may interact with several bacterial families remain to be fully elucidated.

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