Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

Guo, Xianfeng; Li, Shenghui; Zhang, Jiachun; Wu, Feng; Li, Xiangchun; Wu, Dan; Zhang, Min; Ou, Zihao; Jie, Zhuye; Yan, Qiulong; Li, Peng; Yi, Jiangfeng; Peng, Yongzheng

doi:10.1186/s12864-017-4195-3

Cited by 123 publications

(155 citation statements)

References 61 publications

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“…Hence, we focused our attention to the kinetic characterization of the A. muciniphila NagB homologue. It should be noted that the recent genome sequencing of 39 A. muciniphila isolates might result in the discovery of genes coding for a functional NagB homologue, especially because of the great differences found between strains in the amino sugar metabolism (Guo et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

Model‐driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

Ark

Aalvink

Suárez-Diez

et al. 2018

Microbial Biotechnology

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SummaryThe abundance of the human intestinal symbiont Akkermansia muciniphila has found to be inversely correlated with several diseases, including metabolic syndrome and obesity. A. muciniphila is known to use mucin as sole carbon and nitrogen source. To study the physiology and the potential for therapeutic applications of this bacterium, we designed a defined minimal medium. The composition of the medium was based on the genome‐scale metabolic model of A. muciniphila and the composition of mucin. Our results indicate that A. muciniphila does not code for GlmS, the enzyme that mediates the conversion of fructose‐6‐phosphate (Fru6P) to glucosamine‐6‐phosphate (GlcN6P), which is essential in peptidoglycan formation. The only annotated enzyme that could mediate this conversion is Amuc‐NagB on locus Amuc_1822. We found that Amuc‐NagB was unable to form GlcN6P from Fru6P at physiological conditions, while it efficiently catalyzed the reverse reaction. To overcome this inability, N‐acetylglucosamine needs to be present in the medium for A. muciniphila growth. With these findings, the genome‐scale metabolic model was updated and used to accurately predict growth of A. muciniphila on synthetic media. The finding that A. muciniphila has a necessity for GlcNAc, which is present in mucin further prompts the adaptation to its mucosal niche.

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Section: Resultsmentioning

confidence: 99%

Model‐driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

Ark

Aalvink

Suárez-Diez

et al. 2018

Microbial Biotechnology

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“…Recently, Guo et al . () reported a high genetic diversity of A. muciniphila by whole‐genome sequencing, with 5644 unique proteins assembling a flexible open pangenome. They further classified A. muciniphila into three species‐level phylogroups, which demonstrated different function features.…”

Section: Characteristics Of a Muciniphilamentioning

confidence: 99%

“…The genome of A. muciniphila strain MucT (=ATCC BAA-835T=CIP 107961T) involves one circular chromosome of 2.66 Mbp, which shared a limited number of genes (29%) with its closest relatives in the Verrucomicrobia phylum (van Passel et al, 2011). Recently, Guo et al (2017) reported a high genetic diversity of A. muciniphila by whole-genome sequencing, with 5644 unique proteins assembling a flexible open pangenome. They further classified A. muciniphila into three species-level phylogroups, which demonstrated different function features.…”

Section: Characteristics Of a Muciniphilamentioning

confidence: 99%

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Akkermansia muciniphila is a promising probiotic

Zhang

Cheng

et al. 2019

Microbial Biotechnology

529

331

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Summary Akkermansia muciniphila (A. muciniphila), an intestinal symbiont colonizing in the mucosal layer, is considered to be a promising candidate as probiotics. A. muciniphila is known to have an important value in improving the host metabolic functions and immune responses. Moreover, A. muciniphila may have a value in modifying cancer treatment. However, most of the current researches focus on the correlation between A. muciniphila and diseases, and little is known about the causal relationship between them. Few intervention studies on A. muciniphila are limited to animal experiments, and limited studies have explored its safety and efficacy in humans. Therefore, a critical analysis of the current knowledge in A. muciniphila will play an important foundation for it to be defined as a new beneficial microbe. This article will review the bacteriological characteristics and safety of A. muciniphila, as well as its causal relationship with metabolic disorders, immune diseases and cancer therapy.

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“…Recently, a pangenomic study that included 33 new isolates from adults and 6 from laboratory mice provided insights into the population structure and evolutionary history of the Akkermansia lineage [14]. Specifically, this study revealed an open pangenome with at least three species-level phylogroups (AmI, AmII, and AmIII) that appear to be evolving independently.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics guides elucidation of vitamin B12 biosynthesis in novel human associatedAkkermansia

Kirmiz

Galindo

Cross

et al. 2019

Preprint

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22Background: Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most 23 healthy humans and is considered a 'next-generation probiotic.' However, knowledge of the 24 genomic and physiological diversity of human associated Akkermansia is limited, as only one 25 species has been formally described. 26Results: To begin to fill this knowledge gap, we reconstructed 35 high-quality metagenome 27 assembled genomes from children and combined them with 40 other publicly available genomes 28 from adults and mice for comparative genomic analysis. We identified at least four species-level 29 phylogroups (AmI-AmIV) with distinct functional potentials. Most notably, we identified the 30 presence of putative cobalamin (vitamin B12) biosynthesis genes within the AmII (n=26/28) and 31AmIII (n=2/2) phylogroups. To test these predictions, 10 novel strains of Akkermansia were 32 isolated from adults and screened for essential vitamin B12 biosynthesis genes via PCR. Two 33 strains of the AmII phylogroup were positive for the presence of vitamin B12 biosynthesis genes, 34 while all AmI strains, including the type strain A. muciniphila Muc T , were negative. To 35 demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and 36 propionate in the presence and absence of vitamin supplementation in representative strains of 37 the AmI and AmII phylogroups since cobalamin is a cofactor in propionate metabolism. Results 38show that the Akkermansia AmII strain produced acetate and propionate in the absence of 39 supplementation, which is indicative of de novo vitamin B12 biosynthesis. In contrast, acetate 40 and succinate were the main fermentation products for the AmI strains when vitamin B12 was 41 not supplied in the culture medium. 42 Conclusions: We identified Akkermansia strains as potentially important vitamin B12 43 biosynthetic bacteria in the human gut. This novel physiological trait of human associated 44 Akkermansia may impact how these bacteria interact with the human host and other members of 45 the human gut microbiome. 46 47 KEYWORDS: Akkermansia, intestinal bacteria, vitamin B12, human gut microbiome, 48 probiotics 49 50 BACKGROUND 51Akkermansia muciniphila is a mucin degrading, gram-negative intestinal bacterium 52 widely present in the human population, typically at 1 to 4% relative abundance [1, 2]. A number 53 of studies in humans [3-5] and rodents [6][7][8] have found positive associations between its 54 abundance and intestinal health, suggesting that Akkermansia may be a beneficial member of the 55 gut microbiome and could be used as a biomarker of a healthy gut [9][10][11]. However, despite a 56 diversity of phylotypes being reported by previous sequence-based studies, A. muciniphila Muc T 57 (ATCC BAA-835) represents the sole described species of the Verrucomicrobia phylum 58 associated with humans [2, 12, 13]. Therefore, before we can fully assess the health potential of 59 human associated Akkermansia, a comprehensive understanding of the genomic and 60 physiol...

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Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas

Cited by 123 publications

References 61 publications

Model‐driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

Model‐driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

Akkermansia muciniphila is a promising probiotic

Comparative genomics guides elucidation of vitamin B12 biosynthesis in novel human associatedAkkermansia

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