An enzymatic pathway in the human gut microbiome that converts A to universal O type blood

Rahfeld, Peter; Sim, Lyann; Moon, Haisle; Constantinescu, Iren; Morgan-Lang, Connor; Hallam, Steven J.; Kizhakkedathu, Jayachandran N.; Withers, Stephen G.

doi:10.1038/s41564-019-0469-7

Cited by 75 publications

(82 citation statements)

References 61 publications

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“…Interestingly, B. bifidum does not have a gene encoding GH109 α-N-acetylgalactosaminidase that acts on the blood group antigen A [69]. A recent report [70] has shown that gut microbial enzymes convert A-antigens via a novel mechanism to H-antigens through a galactosamine intermediate involving a deacetylase and a GH36 galactosaminidase. Although B. bifidum has one GH36 gene, it likely encodes for raffinose synthase.…”

Section: Glycoside Hydrolases Involved In the Degradation Of Hmos/mucmentioning

confidence: 99%

Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules

et al. 2020

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Certain species of the genus Bifidobacterium represent human symbionts. Many studies have shown that the establishment of symbiosis with such bifidobacterial species confers various beneficial effects on human health. Among the more than ten (sub)species of human gut-associated Bifidobacterium that have significantly varied genetic characteristics at the species level, Bifidobacterium bifidum is unique in that it is found in the intestines of a wide age group, ranging from infants to adults. This species is likely to have adapted to efficiently degrade host-derived carbohydrate chains, such as human milk oligosaccharides (HMOs) and mucin O-glycans, which enabled the longitudinal colonization of intestines. The ability of this species to assimilate various host glycans can be attributed to the possession of an adequate set of extracellular glycoside hydrolases (GHs). Importantly, the polypeptides of those glycosidases frequently contain carbohydrate-binding modules (CBMs) with deduced affinities to the target glycans, which is also a distinct characteristic of this species among members of human gut-associated bifidobacteria. This review firstly describes the prevalence and distribution of B. bifidum in the human gut and then explains the enzymatic machinery that B. bifidum has developed for host glycan degradation by referring to the functions of GHs and CBMs. Finally, we show the data of co-culture experiments using host-derived glycans as carbon sources, which underpin the interesting altruistic behavior of this species as a cross-feeder.

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Section: Glycoside Hydrolases Involved In the Degradation Of Hmos/mucmentioning

confidence: 99%

Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules

et al. 2020

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“…In particular, we selected putative enzymes from the GH5 and GH109 families. The former includes many glucanases involved in polysaccharide hydrolysis and could be of great interest for biotechnological applications such as in the second-generation biorefineries, while in GH109, which are particularly interesting for the removal of a-GlcNAc from the antigens from red blood cells [72,73], members from Archaea have never been identified. Pool1 Pool2 GT2 62 65 GT4 83 81 GT5 9 11 GT20 2 0 GT21 3 5 GT35 3 5 GT66 5 6 GH1 6 5 GH2 0 1 GH3 3 2 GH4 2 0 GH5 1 4 GH12 4 8 GH13 7 10 GH15 16 27 GH29 0 1 GH31 7 9 GH36 1 5 GH38 13 8 GH57 15 12…”

Section: Gh99 Gh130 Inmentioning

confidence: 99%

Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments

et al. 2019

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The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy), to discover hyperthermophilic carbohydrate‐active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here, we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T = 85 °C and pH 5.5; T = 92 °C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in silico analysis led to 14 934 and 17 652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarchaeota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~ 2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β‐mannanase/β‐1,3‐glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+‐dependent GH109 with a previously unreported β‐N‐acetylglucosaminide/β‐glucoside specificity. Databases The sequencing reads are available in the NCBI Sequence Read Archive (SRA) database under the accession numbers SRR7545549 (Pool1) and SRR7545550 (Pool2). The sequences of GH5_Pool2 and GH109_Pool2 are available in GenBank database under the accession numbers MK869723 and MK86972, respectively. The environmental data relative to Pool1 and Pool2 (NCBI BioProject PRJNA481947) are available in the Biosamples database under the accession numbers SAMN09692669 (Pool1) and SAMN09692670 (Pool2).

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“…Genetic studies of the gut microbiota have not yet reported genome-wide significant associations with ABO blood type genes themselves 51–54 , while multiple studies have reported impact of FUT2 secretor/non-secretor status on gut microbiota composition 55–57 . Tentative associations here are yet to be matched with in vitro studies with the glycans 58, 59 .…”

Section: Discussionmentioning

confidence: 99%

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

Jie

Liang

Ding

et al. 2019

Preprint

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1 More than a decade of gut microbiome studies have a common goal for human 2 health. As most of the disease studies sample the elderly or the middle-aged, a 3 reference cohort for young individuals has been lacking. It is also not clear what 4 other omics data need to be measured to better understand the gut microbiome.5 Here we present high-depth metagenomic shotgun sequencing data for the fecal 6 microbiome together with other omics data in a cohort of 2,183 adults, and observe 7 a number of vitamins, hormones, amino acids and trace elements to correlate with 8 the gut microbiome and cluster with T cell receptors. Associations with physical 9 fitness, sleeping habits and dairy consumption are identified in this large multi-omic 1 0 cohort. Many of the associations are validated in an additional cohort of 1,404 1 1 individuals. Our comprehensive data are poised to advise future study designs to 1 2 better understand and manage our gut microbiome both in population and in 1 3 mechanistic investigations.

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An enzymatic pathway in the human gut microbiome that converts A to universal O type blood

Cited by 75 publications

References 61 publications

Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules

Enzymatic Adaptation of Bifidobacterium bifidum to Host Glycans, Viewed from Glycoside Hydrolyases and Carbohydrate-Binding Modules

Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

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