Clostridioides difficileuses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea

The gut microbiota plays a critical role in pathogen defense. Studies using antibiotic-treated mice reveal mechanisms that increase susceptibility toClostridioides difficileinfection (CDI), but risk factors associated with CDI in humans extend beyond antibiotic use. Here, we studied the dysbiotic gut microbiota of a subset of patients with diarrhea and modeled the gut microbiota of these patients by fecal transplantation into germ-free mice. When challenged withC. difficile, the germ-free mice transplanted with fecal samples from patients with dysbiotic microbial communities showed increased gut amino acid concentrations and greater susceptibility to CDI. AC. difficilemutant that was unable to use proline as an energy source was unable to robustly infect germ-free mice transplanted with a dysbiotic or healthy human gut microbiota. Prophylactic dietary intervention using a low-proline or low-protein diet in germ-free mice colonized by a dysbiotic human gut microbiota resulted in decreased expansion of wild-typeC. difficileafter challenge, suggesting that amino acid availability might be important for CDI. Furthermore, a prophylactic fecal microbiota transplant in mice with dysbiosis reduced proline availability and protected the mice from CDI. Last, we identified clinical risk factors that could potentially predict gut microbial dysbiosis and thus greater susceptibility to CDI in a retrospective cohort of patients with diarrhea. Identifying at-risk individuals and reducing their susceptibility to CDI through gut microbiota–targeted therapies could be a new approach to preventingC. difficileinfection in susceptible patients.

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Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.014974 ◽

2020 ◽

Vol 295 (52) ◽

pp. 18625-18637

Author(s):

Cheng-Jie Duan ◽

Arnaud Baslé ◽

Marcelo Visona Liberato ◽

Joseph Gray ◽

Sergey A. Nepogodiev ◽

...

Keyword(s):

Gut Microbiota ◽

Critical Role ◽

Pectin Methylesterase ◽

Bacteroides Thetaiotaomicron ◽

Human Gut ◽

Human Gut Microbiota ◽

New Family ◽

Gut Microbe ◽

Dietary Nutrient ◽

Helical Proteins

Pectins are a major dietary nutrient source for the human gut microbiota. The prominent gut microbe Bacteroides thetaiotaomicron was recently shown to encode the founding member (BT1017) of a new family of pectin methylesterases essential for the metabolism of the complex pectin rhamnogalacturonan-II (RG-II). However, biochemical and structural knowledge of this family is lacking. Here, we showed that BT1017 is critical for the metabolism of an RG-II–derived oligosaccharide ΔBT1017oligoB generated by a BT1017 deletion mutant (ΔBT1017) during growth on carbohydrate extract from apple juice. Structural analyses of ΔBT1017oligoB using a combination of enzymatic, mass spectrometric, and NMR approaches revealed that it is a bimethylated nonaoligosaccharide (GlcA-β1,4-(2-O-Me-Xyl-α1,3)-Fuc-α1,4-(GalA-β1,3)-Rha-α1,3-Api-β1,2-(Araf-α1,3)-(GalA-α1,4)-GalA) containing components of the RG-II backbone and its side chains. We showed that the catalytic module of BT1017 adopts an α/β-hydrolase fold, consisting of a central twisted 10-stranded β-sheet sandwiched by several α-helices. This constitutes a new fold for pectin methylesterases, which are predominantly right-handed β-helical proteins. Bioinformatic analyses revealed that the family is dominated by sequences from prominent genera of the human gut microbiota, including Bacteroides and Prevotella. Our re-sults not only highlight the critical role played by this family of enzymes in pectin metabolism but also provide new insights into the molecular basis of the adaptation of B. thetaiotaomicron to the human gut.

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Genetically Obese Human Gut Microbiota Induces Liver Steatosis in Germ-Free Mice Fed on Normal Diet

Frontiers in Microbiology ◽

10.3389/fmicb.2018.01602 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 13

Author(s):

Ruirui Wang ◽

Hui Li ◽

Xin Yang ◽

Xinhe Xue ◽

Liman Deng ◽

...

Keyword(s):

Gut Microbiota ◽

Liver Steatosis ◽

Normal Diet ◽

Human Gut ◽

Germ Free ◽

Human Gut Microbiota ◽

Obese Human

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Consistent alterations of human fecal microbes after transplanted to germ-free mice

10.1101/495663 ◽

2018 ◽

Cited By ~ 1

Author(s):

Yanze Li ◽

Wenming Cao ◽

Na L Gao ◽

Xing-Ming Zhao ◽

Wei-Hua Chen

Keyword(s):

Mouse Model ◽

Gut Microbiota ◽

Fecal Microbiota ◽

Species Level ◽

Human Gut ◽

Fecal Microbiota Transplant ◽

Change Rate ◽

Gut Microbes ◽

Germ Free ◽

Human And Mouse

AbstractBackgroundFecal microbiota transplant (FMT) of human fecal samples to germ-free (GF) mice is useful for establishing causal relationships between gut microbiota and human phenotypes. However, due to intrinsic differences between human and mouse intestines and distinct diets between the two organisms, replicating human phenotypes in mouse through FMT is not guaranteed; similarly, treatments that are effective in mouse models do not guarantee their success in human either.ResultsIn this study, we aimed to identify human gut microbes that have undergone significant and consistent changes after transplanted to GF mice across multiple experimental settings. By comparing gut microbiota profiles in 1,713 human-mouse pairs, we found strikingly on average <50% of the human gut microbes can be re-established in mice at the species level; among which, more than 1/3 have undergone significant changes (referred as to “variable microbes”), most of which were consistent across multiple human-mouse pairs and experimental settings. Consistently, one-third of human samples had changed their enterotypes, i.e. significant changes in their leading species after FMT. Mice fed with controlled diet showed significant decrease in the enterotype change rate (~25%) as compared those with non-controlled diet (~50%), suggesting a possible solution for rescue. Strikingly, most of the variable microbes have been implicated in human diseases, with some being recognized as causing species.ConclusionsOur results highlighted the challenges of using mouse model in replicating human gut microbiota-associated phenotypes, provided useful information for researchers using mice in their gut microbiota studies and call for additional validations after FMT.

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Carrageenan oligosaccharides and their degrading bacteria induce intestinal inflammation in germ-free mouse

10.21203/rs.3.rs-26790/v1 ◽

2020 ◽

Author(s):

Yeshi Yin ◽

Miaomiao Li ◽

Weizhong Gu ◽

Benhua Zeng ◽

Wei Liu ◽

...

Keyword(s):

Inflammatory Response ◽

Gut Microbiota ◽

Fecal Microbiota ◽

Rna Seq ◽

Human Gut ◽

Germ Free ◽

Esi Ms ◽

Human Gut Microbiota ◽

Degrading Bacteria

Abstract Background: Carrageenans (CGNs) are widely used in food and pharmaceutical industries. However, the safety of CGNs is still under debate, because degraded CGNs have been reported to promote an intestinal inflammatory response in animal models. Here, we studied the relationship among CGNs, human gut microbiota, and the host inflammatory response.Methods: TLC was selected for detecting the degradation of KCPs by human gut microbiota in vitro batch fermentation system. PCR-DGGE and real time PCR were used for studying bacterial community. ESI-MS was used for KCPs structure analysis. Hematoxylin-eosin staining (HE), immunohistochemistry (IHC) and RNA-seq were used to evaluated the KCPs on host inflammation response in germ-free mice.Results: Thin-layer chromatography (TLC) data showed that CGNs with a molecular weight (Mw) higher than 100 kDa are not degraded by human fecal microbiota, but low Mw CGNs with an Mw around ~4.5 kDa (KCOs) could be degraded by seven of eight human fecal microbiota samples. KCO degrading B. xylanisolvens was isolated from fecal samples, and PCR-DGGE profiling with band sequencing suggested that B. xylanisolvens was the key KCO degrader in the human gut. Two putative κ-carrageenase genes were identified in the genome sequence of B. xylanisolvens. However, their function on KCO degrading was not verified in vitro. And the sulfate group from KCO is not removed after in vitro degradation by human fecal microbiota, as shown by ESI-MS analysis. The effects of KCO and KCO degrading bacteria on the inflammatory response were investigated in germ-free mice. Increased numbers of P-P38-, CD3a-, and CD79a-positive cells were found in the colon and rectum in mice fed with KCO plus KCO degrading bacteria than in mice fed with only KCO or only B. xylanisolvens and E. coli, as shown by RNA-Seq analysis, HE staining, and IHC. Conclusion: Our data suggested that the presence of KCO degrading bacteria promote the pro-inflammatory effects of CGNs.

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25 Colonization of Germ-Free Mice by Human Gut Microbiota Alters Colonic Morphology and Increases Tph1 Expression Likely Contributing to Altered Colonic Contractility Following Colonization

Gastroenterology ◽

10.1016/s0016-5085(14)60025-1 ◽

2014 ◽

Vol 146 (5) ◽

pp. S-7-S-8

Author(s):

Christopher S. Reigstad ◽

Charles E. Salmonson ◽

David R. Linden ◽

Joseph H. Szurszewski ◽

Justin L. Sonnenburg ◽

...

Keyword(s):

Gut Microbiota ◽

Human Gut ◽

Germ Free ◽

Human Gut Microbiota

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Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease

10.1101/600155 ◽

2019 ◽

Cited By ~ 3

Author(s):

Renuka R. Nayak ◽

Margaret Alexander ◽

Kye Stapleton-Grey ◽

Carles Ubeda ◽

Jose U. Scher ◽

...

Keyword(s):

Gut Microbiota ◽

Drug Response ◽

Ex Vivo ◽

Critical Role ◽

Pharmaceutical Drugs ◽

Human Gut ◽

Human Gut Microbiota ◽

Antibiotic Drug ◽

Target Effects

AbstractThe trillions of microorganisms (microbiota) found within the human gut play a critical role in shaping the immune system, yet these complex microbial communities are also highly sensitive to numerous environmental factors. While much of the focus to date has been on dietary intake, emerging data has begun to suggest that the use of pharmaceutical drugs, even those that are not considered to be antibiotics, can alter the human gut microbiota with unknown consequences for treatment outcomes. Here, we use a combination ofin vitro, in vivo, andex vivomethods to demonstrate that the first-line therapy for rheumatoid arthritis (RA), methotrexate (MTX), has off-target effects on the human gut microbiota, resulting in a significant growth advantage for drug-resistant Firmicutes over the Bacteroidetes, which tend to be more sensitive. Longitudinal analyses of the gut microbiotas of RA patients revealed that MTX-induced shifts in bacterial relative abundance are associated with improved drug response and transplant experiments in gnotobiotic mice show that these shifts lead to reduced inflammation. Together, these results suggest that the mechanism-of-action of non-antibiotic drugs may be due in part to off-target effects on the gut microbiota, while providing a critical first step towards explaining long-standing differences in drug response between patients.

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Lysozyme-like Protein Produced by Bifidobacterium longum Regulates Human Gut Microbiota Using In Vitro Models

Molecules ◽

10.3390/molecules26216480 ◽

2021 ◽

Vol 26 (21) ◽

pp. 6480

Author(s):

Mingzhu Du ◽

Xinqiang Xie ◽

Shuanghong Yang ◽

Ying Li ◽

Tong Jiang ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Gut Microbiota ◽

Bifidobacterium Longum ◽

16S Rrna Genes ◽

Rrna Genes ◽

Human Gut ◽

Human Gut Microbiota ◽

M1 Protein

The extracellular secreted protein of Bifidobacterium longum (B. longum) plays an important role in maintaining the homeostasis of the human intestinal microenvironment. However, the mechanism(s) of interaction remain unclear. Lysozyme is a kind of antibacterial peptide. In this study, the amino acid sequence of a lysozyme-like protein of B. longum based on whole-genome data of an isolate from human gut feces was found. We further predicted functional domains from the amino acid sequence, purified the protein, and verified its bioactivity. The growth of some bacteria were significantly delayed by the 020402_LYZ M1 protein. In addition, the gut microbiota was analyzed via high-throughput sequencing of 16S rRNA genes and an in vitro fermentation model, and the fluctuations in the gut microbiota under the treatment of 020402_LYZ M1 protein were characterized. The 020402_LYZ M1 protein affected the composition of human gut microbiota significantly, implying that the protein is able to communicate with intestinal microbes as a regulatory factor.

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