Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets

Onishi, Janet C.; Campbell, Sara C.; Moreau, Michael M.; Patel, Falshruti B.; Brooks, Andrew I.; Zhou, Yin; Häggblom, Max M.; Storch, Judith

doi:10.1099/mic.0.000496

Cited by 38 publications

(41 citation statements)

References 43 publications

(49 reference statements)

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“…Due to the strong correlative relationship between the QTL, we tested whether there was a direct interaction between bile acids and Turicibacter . Turicibacter inhabits the small intestine where BAs are secreted upon consumption of a meal (73,74). We screened the human isolate Turicibacter sanguinis for deconjugation and transformation activity in vitro by HPLC/MS-MS. We found that T. sanguinis deconjugated ∼96-100% of taurocholic acid and glycochenodeoxycholic acid (Fig 5A) within 24 hours.…”

Section: Resultsmentioning

confidence: 99%

Genetic determinants of gut microbiota composition and bile acid profiles in mice

Kemis

Linke

Barrett

et al. 2019

Preprint

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26 The microbial communities that inhabit the distal gut of humans and other mammals exhibit large 27 inter-individual variation. While host genetics is a known factor that influences gut microbiota 28 composition, the mechanisms underlying this variation remain largely unknown. Bile acids (BAs) 29 are hormones that are produced by the host and chemically modified by gut bacteria. BAs serve as 30 environmental cues and nutrients to microbes, but they can also have antibacterial effects. We 31 hypothesized that host genetic variation in BA metabolism and homeostasis influence gut 32 microbiota composition. To address this, we used the Diversity Outbred (DO) stock, a population 33 of genetically distinct mice derived from eight founder strains. We characterized the fecal 34 microbiota composition and plasma and cecal BA profiles from 400 DO mice maintained on a 35 high-fat high-sucrose diet for ~22 weeks. Using quantitative trait locus (QTL) analysis, we 36 identified several genomic regions associated with variations in both bacterial and BA profiles.37 Notably, we found overlapping QTL for Turicibacter sp. and plasma cholic acid, which mapped 38 to a locus containing the gene for the ileal bile acid transporter, Slc10a2. Mediation analysis and 39 subsequent follow-up validation experiments suggest that differences in Slc10a2 gene expression 40 associated with the different strains influences levels of both traits and revealed novel interactions 41 between Turicibacter and BAs. This work illustrates how systems genetics can be utilized to 42 generate testable hypotheses and provide insight into host-microbe interactions. 44Author summary 45 Inter-individual variation in the composition of the intestinal microbiota can in part be attributed 46 to host genetics. However, the specific genes and genetic variants underlying differences in the 47 microbiota remain largely unknown. To address this, we profiled the fecal microbiota composition 3 48 of 400 genetically distinct mice, for which genotypic data is available. We identified many loci of 49 the mouse genome associated with changes in abundance of bacterial taxa. One of these loci is 50 also associated with changes in the abundance of plasma bile acidsmetabolites generated by the 51 host that influence both microbiota composition and host physiology. Follow up validation 52 experiments provide mechanistic insights linking host genetic differences, with changes in ileum 53 gene expression, bile acid-bacteria interactions and bile acid homeostasis. Together, this work 54 demonstrates how genetic approaches can be used to generate testable hypothesis to yield novel 55 insight into how host genetics shape gut microbiota composition. 56 57 Introduction 58The intestinal microbiota has profound effects on host physiology and health (1-3). The 59 composition of the gut microbiota is governed by a combination of environmental factors, 60 including diet, drugs, maternal seeding, cohabitation, and host genetics (4-7). Together, these 61 factors cause substantial inter-i...

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Section: Resultsmentioning

confidence: 99%

Genetic determinants of gut microbiota composition and bile acid profiles in mice

Kemis

Linke

Barrett

et al. 2019

Preprint

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“…These microorganisms may promote intestinal homeostasis and may protect against inflammatory diseases [54][55][56][57]. Vitamin B12 is absorbed in the small intestines [58][59][60] while the majority of microbiota reside in the colon [58], although, the small intestine is not sterile and does contain a robust microbiota that influences the absorption of vitamins [61][62][63]. Specific bacteria produce vitamin B12 [64], and the children infected with G. duodenalis with DNA levels above 1 fg/µl may be unable to synthesize the required amounts of vitamin B12 for nutritional benefit.…”

Section: Changes In Vitamin B12 Due To Parasite Infectionsmentioning

confidence: 99%

Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study

et al. 2020

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Background: Approximately 30% of children worldwide are infected with gastrointestinal parasites. Depending on the species, parasites can disrupt intestinal bacterial microbiota affecting essential vitamin biosynthesis.Methods: Stool samples were collected from 37 asymptomatic children from a previous cross-sectional Argentinian study. A multi-parallel real-time quantitative PCR was implemented for Ascaris lumbricoides, Ancylostoma duodenale, Necator americanus, Strongyloides stercoralis, Trichuris trichiura, Cryptosporidium spp., Entamoeba histolytica and Giardia duodenalis. In addition, whole-genome sequencing analysis was conducted for bacterial microbiota on all samples and analyzed using Livermore Metagenomic Analysis Toolkit and DIAMOND software. Separate analyses were carried out for uninfected, Giardia-only, Giardia + helminth co-infections, and helminth-only groups. Results:For Giardia-only infected children compared to uninfected children, DNA sequencing data showed a decrease in microbiota biodiversity that correlated with increasing Giardia burden and was statistically significant using Shannonʼs alpha diversity (Giardia-only > 1 fg/µl 2.346; non-infected group 3.253, P = 0.0317). An increase in diversity was observed for helminth-only infections with a decrease in diversity for Giardia + helminth co-infections (P = 0.00178). In Giardia-only infections, microbiome taxonomy changed from Firmicutes towards increasing proportions of Prevotella, with the degree of change related to the intensity of infection compared to uninfected (P = 0.0317). The abundance of Prevotella bacteria was decreased in the helminths-only group but increased for Giardia + helminth co-infections (P = 0.0262). Metagenomic analysis determined cobalamin synthesis was decreased in the Giardia > 1 fg/µl group compared to both the Giardia < 1 fg/µl and the uninfected group (P = 0.0369). Giardia + helminth group also had a decrease in cobalamin CbiM genes from helminth-only infections (P = 0.000754). Conclusion:The study results may provide evidence for an effect of parasitic infections enabling the permissive growth of anaerobic bacteria such as Prevotella, suggesting an altered capacity of vitamin B12 (cobalamin) biosynthesis and potential impact on growth and development in children .

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“…Moreover, the microvasculature of the SB comprises a rich network of capillaries that lie in the submucosal layer of the SB, allowing for rapid absorption of nutrients such as amino acids, fatty acids, and monosaccharides (160) into the bloodstream and distribution to the other organs (157)(158)(159). The SB contains a relatively lesser number of bacteria, with the major phyla being Bacteriodetes, Firmicutes, and Proteobacteria and anaerobes such as Lactobacillus species being the most predominant genera (161). The colon, on the other hand, averages at about 1.5-2 m in humans and consists of 6 sections, beginning with the cecum and followed by the ascending colon, transverse colon, descending colon, the S-shaped sigmoid colon, and, lastly, the rectum.…”

Section: Function Of the Gutmentioning

confidence: 99%

The PPAR–microbiota–metabolic organ trilogy to fine‐tune physiology

Visvalingam

Wahli

2019

FASEB j.

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The human gut is colonized by commensal microorganisms, predominately bacteria that have coevolved in symbiosis with their host. The gut microbiota has been extensively studied in recent years, and many important findings on how it can regulate host metabolism have been unraveled. In healthy individuals, feeding timing and type of food can influence not only the composition but also the circadian oscillation of the gut microbiota. Host feeding habits thus influence the type of microbe‐derived metabolites produced and their concentrations throughout the day. These microbe‐derived metabolites influence many aspects of host physiology, including energy metabolism and circadian rhythm. Peroxisome proliferator‐activated receptors (PPARs) are a group of ligand‐activated transcription factors that regulate various metabolic processes such as fatty acid metabolism. Similar to the gut microbiota, PPAR expression in various organs oscillates diurnally, and studies have shown that the gut microbiota can influence PPAR activities in various metabolic organs. For example, short‐chain fatty acids, the most abundant type of metabolites produced by anaerobic fermentation of dietary fibers by the gut microbiota, are PPAR agonists. In this review, we highlight how the gut microbiota can regulate PPARs in key metabolic organs, namely, in the intestines, liver, and muscle. Knowing that the gut microbiota impacts metabolism and is altered in individuals with metabolic diseases might allow treatment of these patients using noninvasive procedures such as gut microbiota manipulation.—Oh, H. Y. P., Visvalingam, V., Wahli, W. The PPAR–microbiota–metabolic organ trilogy to fine‐tune physiology. FASEB J. 33, 9706–9730 (2019). http://www.fasebj.org

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Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets

Cited by 38 publications

References 43 publications

Genetic determinants of gut microbiota composition and bile acid profiles in mice

Genetic determinants of gut microbiota composition and bile acid profiles in mice

Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study

The PPAR–microbiota–metabolic organ trilogy to fine‐tune physiology

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