Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways

Pichler, Michael Jakob; Yamada, Chihaya; Shuoker, Bashar; Alvarez-Silva, Camila; Gotoh, Aina; Leth, Maria Louise; Schoof, Erwin M.; Katoh, Toshihiko; Sakanaka, Mikiyasu; Katayama, Takane; Jin, Chunsheng; Karlsson, Niclas G.; Arumugam, Manimozhiyan; Fushinobu, Shinya; Hachem, Maher Abou

doi:10.1038/s41467-020-17075-x

Cited by 116 publications

(89 citation statements)

References 81 publications

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“…Our associations of Faecalicatena lactaris ( p =1.10×10 -12 ) and CoUinsella ( p =2.59×10 -8 ) with ABO suggest a possible metabolic link with blood antigens. A comparison of CAZyme profiles across a set of reference genomes revealed 3 CAZymes with blood-related activities in F. lactaris (GH110 45 , GH136 46 , CBM32 47 ), but none in any of 9 Collinsella species ( Figure 3A ). More mucus-targeting and less fiber-degrading enzymes were found in F. lactaris than Collinsella ( Figure 3A ), suggesting distinct functions in the gut.…”

Section: Resultsmentioning

confidence: 99%

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Qin

Havulinna

Liu

et al. 2020

Preprint

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Co-evolution between humans and the microbial communities colonizing them has resulted in an intimate assembly of thousands of microbial species mutualistically living on and in their body and impacting multiple aspects of host physiology and health. Several studies examining whether human genetic variation can affect gut microbiota suggest a complex combination of environmental and host factors. Here, we leverage a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial shotgun metagenomes, dietary information and health records up to 16 years post-sampling, to characterize human genetic variations associated with microbial abundances, and predict possible causal links with various diseases using Mendelian randomization (MR). Genome-wide association study (GWAS) identified 583 independent SNP-taxon associations at genome-wide significance (p<5.0×10-8), which included notable strong associations with LCT (p=5.02×10-35), ABO (p=1.1×10-12), and MED13L (p=1.84×10-12). A combination of genetics and dietary habits was shown to strongly shape the abundances of certain key bacterial members of the gut microbiota, and explain their genetic association. Genetic effects from the LCT locus on Bifidobacterium and three other associated taxa significantly differed according to dairy intake. Variation in mucin-degrading Faecalicatena lactaris abundances were associated with ABO, highlighting a preferential utilization of secreted A/B/AB-antigens as energy source in the gut, irrespectively of fibre intake. Enterococcus faecalis levels showed a robust association with a variant in MED13L, with putative links to colorectal cancer. Finally, we identified putative causal relationships between gut microbes and complex diseases using MR, with a predicted effect of Morganella on major depressive disorder that was consistent with observational incident disease analysis. Overall, we present striking examples of the intricate relationship between humans and their gut microbial communities, and highlight important health implications.

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Section: Resultsmentioning

confidence: 99%

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Qin

Havulinna

Liu

et al. 2020

Preprint

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“…Butyrate producing Clostridiales bacterium is associated in protection of host from colorectal cancer, immune, and metabolic disorders [60]. It means dropped Clostridiales bacterium in yaks made contribute to diarrhea.…”

Section: Discussionmentioning

confidence: 99%

Effects of Short Chain Fatty Acids (SCFAs) Modulation on Potentially Diarrhea Causing Pathogens in Yaks Through Metagenomics Sequencing

Li¹,

Zeng²,

Liu³

et al. 2020

Preprint

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Yaks are of great importance on the plateau; however, an emerging endemic diarrheal disease during the last few years is posing a great threat to the health of these animals. Yaks have special gut microbiotal community and short-chain fatty acids (SCFAs) which are not only the principle nutrient substrates of intestinal epithelial cells but can also regulate the epithelial barrier. Until now, metagenomics sequencing has not been reported in diarrheal yaks. A scarce information is available regarding the levels of fecal SCFAs and diarrhea in yaks. The purpose of our study was to identify the potential pathogens that cause the emerging diarrhea and also to explore the potential relationship of short-chain fatty acids in this issue. We estimated diarrhea rate in yaks after collecting the equal number of fecal samples from affected animals. Metagenomics sequencing and quantitative analysis of SCFAs were performed which revealed 15-25% and 5-10% prevalence in diarrheal yak’s calves and adults yaks respectively. Significant difference was observed in GC contents (44.69%~46.08% vs 46.12%~46.38%) under two reference groups (p<0.05). Violin box plot also showed the higher degree of dispersion in gene abundance distribution of diarrhea yaks, while genes of normal yaks were relatively gathered. We found 366163 significant differential abundance genes in diarrheal yaks, with 141305 up-regulated and 224858 down-regulated genes as compared with normal yaks via DESeq analysis. Metagenomic binning analysis indicated the higher significant of bin 33 (Bacteroidales) (p<0.05) in diarrheal animals, while bin 10 (p<0.0001), bin 30 (Clostridiales) (p<0.05), bin 51 (Lactobacillales) (p<0.05), bin 8 (Lachnospiraceae) (p<0.05) and bin 47 (Bacteria) (p<0.05) were obviously higher in normal animals. At different levels, an obviously difference in Phylum, Class, Oder, Family, Genus and Species was noticed as 4, 8, 8, 16, 17 and 30 respectively. Compared with healthy yaks, Acetic acid (p<0.01), Propionic acid (p<0.01), Butyric acid (p<0.01), Isobutyric acid, Isovaleric acid (p<0.05) and Caproic acid (p<0.01) were all observed obviously at lower rate in diarrheal yaks. In conclusion, besides the increased pathogens level of Staphylococcus aureus, Babesia ovata, Anaplasma phagocytophilum, Bacteroides fluxus, viruses, Klebsiella pneumonia, and inflammation-related bacteria; the decreased of SCFAs caused by the imbalance of intestinal microbiota may potentially leads to emergence of diarrhea in yaks.

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“…The exact growth-promoting effect of HMOs on Staphylococcus isolates from human milk remains unknown, since these bacteria do not metabolize these compounds (Hunt et al, 2012). Recently, novel pathways enabling the growth of Roseburia and Eubacterium (two butyrate-producing genera that have been repeteadly detected in human milk) on HMOs have been published (Pichler et al, 2020). More studies are required to elucidate how HMOs can contribute to shape the microbiota of milk.…”

Section: Human Milk Oligosaccharidesmentioning

confidence: 99%

The Microbiota of the Human Mammary Ecosystem

Fernández

Pannaraj

Rautava

et al. 2020

Front. Cell. Infect. Microbiol.

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Human milk contains a dynamic and complex site-specific microbiome, which is not assembled in an aleatory way, formed by organized microbial consortia and networks. Presence of some genera, such as Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium (formerly known as Propionibacterium), Lactobacillus, Lactococcus and Bifidobacterium, has been detected by both culture-dependent and culture-independent approaches. DNA from some gut-associated strict anaerobes has also been repeatedly found and some studies have revealed the presence of cells and/or nucleic acids from viruses, archaea, fungi and protozoa in human milk. Colostrum and milk microbes are transmitted to the infant and, therefore, they are among the first colonizers of the human gut. Still, the significance of human milk microbes in infant gut colonization remains an open question. Clinical studies trying to elucidate the question are confounded by the profound impact of non-microbial human milk components to intestinal microecology. Modifications in the microbiota of human milk may have biological consequences for infant colonization, metabolism, immune and neuroendocrine development, and for mammary health. However, the factors driving differences in the composition of the human milk microbiome remain poorly known. In addition to colostrum and milk, breast tissue in lactating and non-lactating women may also contain a microbiota, with implications in the pathogenesis of breast cancer and in some of the adverse outcomes associated with breast implants. This and other open issues, such as the origin of the human milk microbiome, and the current limitations and future prospects are addressed in this review.

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Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways

Cited by 116 publications

References 81 publications

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Effects of Short Chain Fatty Acids (SCFAs) Modulation on Potentially Diarrhea Causing Pathogens in Yaks Through Metagenomics Sequencing

The Microbiota of the Human Mammary Ecosystem

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