Journal: Genome Biology

Article Title: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

doi: 10.1186/s13059-021-02427-7

Figure Lengend Snippet: The Akkermansia genus comprises four additional candidate species phylogenetically rooted between the already characterized A. glycaniphila and A. muciniphila . A Whole-genome phylogeny of the 2420 metagenome-assembled genomes (MAGs) reconstructed here and the genomes from isolate sequencing available in NCBI taxonomically annotated as A. muciniphila or Akkermansia spp. The phylogenetic tree is rooted using Verrucomicrobium spinosum as an outgroup and was built using PhyloPhlAn 3 with 400 universal markers (see the “Methods” section). SGB, species-level genome bin (see the “Methods” section). B Within- and between-clade whole-genome average estimated nucleotide identity (fastANI , top panels) and full-length 16S sequence distances (bottom panels) among Akkermansia SGBs provide evidence that these are candidate species

Article Snippet: However, experimental Akkermansia research still heavily relies on the type strain A. muciniphila Muc T (ATCC BAA-835) and on a few more genomes of newly isolated strains that became available recently [ – ].

Techniques: Sequencing

Journal: Genome Biology

Article Title: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

doi: 10.1186/s13059-021-02427-7

Figure Lengend Snippet: Prevalence and insights into the ecological and functional characteristics of Akkermansia candidate species. A Akkermansia candidate species have variable prevalence across hosts and wild versus captive mice and non-human primates. We computed prevalences using species-specific marker genes (see the “Methods” section) applied on a total of 13,237 metagenomic samples. B , C Akkermansia candidate species are strongly mutually exclusive (analysis based on 4171 Akkermansia -positive human metagenomes). D A. muciniphila but not the other Akkermansia candidate species is associated with decreased host body mass index (BMI) according to a meta-analysis random effect model of partial correlations adjusted for age and sex (see the “Methods” section) comprising 3311 human metagenomic samples from 22 datasets (Additional file : Table S2). E Corrin ring biosynthesis operon genes are consistently present only in candidate species SGB9227 and SGB9228 (see the “Methods” section). F Growth analysis of the A. muciniphila and A. glycaniphila type strains shows propionate production by Pyt T but not Muc T in the absence of vitamin B12. This is indicative of endogenous production of vitamin B12 (acting as a cofactor for the methyl-malonyl CoA synthase reaction) by Pyt T but not Muc T . G Core gene genetic distances are correlated with corrin ring biosynthesis gene genetic distances. Pairwise distances were computed only for strains in which all genes were found together on the same contig

Article Snippet: However, experimental Akkermansia research still heavily relies on the type strain A. muciniphila Muc T (ATCC BAA-835) and on a few more genomes of newly isolated strains that became available recently [ – ].

Techniques: Functional Assay, Marker

Journal: Genome Biology

Article Title: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

doi: 10.1186/s13059-021-02427-7

Figure Lengend Snippet: The CRISPR-Cas system of Akkermansia candidate species and their viral targets. A CRISPR locus type composition of Akkermansia candidate species. All candidate species possess CRISPR locus type I-C, with the exception of A. muciniphila in which type II-C is present in more than 30% of the genomes. B Representative locus organization of CRISPR loci over Akkermansia candidate species. Some type I-C loci contain only one CRISPR array. Gene and CRISPR array lengths are scaled to correspond to the median length over all loci. C Phylogenetic tree of A. muciniphila subspecies colored by type II-C presence. D The total number of spacer sequences for the genomes in each Akkermansia candidate species. Type II-C loci were only found in A. muciniphila . Numbers above the boxplots correspond to the fraction of type I-C loci with two CRISPR arrays. E Logo plots of predicted PAM sequences in putative (phage) Viral Clusters (VCs, see the “Methods” section) upstream of sequences with perfect matches against CRISPR spacer sequences from type I-C loci. F Proportion of CRISPR spacers within candidate species genomes with a near-perfect match (at most 2 mismatched nucleotides) for four VCs. The number above the box plots corresponds to the fraction of genomes with at least one spacer hit against a given VC (see the “Methods” section). G Mapping of spacers from Akkermansia genomes against two representative VCs, visualized with a sliding window of 150 nt. See Additional file : Figure S8 for the remaining VCs. H Distribution of the relative abundances of the Akkermansia candidate species based on the presence or absence of each cognate VC in the metagenome (Additional file : Table S2, see the “Methods” section). P -values for differential abundance were determined via two-sided Wilcoxon rank-sum tests. P -values of <0.01 were considered significant. The numbers above the box plots correspond to the generalized fold change, with negative numbers indicating a higher bacterial abundance when a VC is detected

Article Snippet: However, experimental Akkermansia research still heavily relies on the type strain A. muciniphila Muc T (ATCC BAA-835) and on a few more genomes of newly isolated strains that became available recently [ – ].

Techniques: CRISPR

Journal: Genome Biology

Article Title: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

doi: 10.1186/s13059-021-02427-7

Figure Lengend Snippet: Functional diversification of A. muciniphila subspecies and cognate exopolysaccharide/LipidA synthesis operon. A Ordination analysis (Jaccard-distance-based PCoA using gene presence and absence information) reveals a diversification of gene repertoires of A. muciniphila subspecies. Genes found in less than 3% of strains were excluded. Subspecies designation is derived from the A. muciniphila phylogenetic tree in Fig. . B Operon archetypes putatively involved in exopolysaccharide/LipidA synthesis in A. muciniphila GP41 (operon archetype 1) and A. muciniphila Muc T (operon archetype 2). C PCoA (same as in A ) colored by operon archetype membership. Genomes in which neither operon could be found were labeled “Unassigned”

Article Snippet: However, experimental Akkermansia research still heavily relies on the type strain A. muciniphila Muc T (ATCC BAA-835) and on a few more genomes of newly isolated strains that became available recently [ – ].

Techniques: Functional Assay, Derivative Assay, Labeling

Journal: Genome Biology

Article Title: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

doi: 10.1186/s13059-021-02427-7

Figure Lengend Snippet: A. muciniphila is stratified in multiple subspecies with distinct host preferences. A Phylogenetic tree of A. muciniphila based on a core-gene alignment built using 169 clade-specific core genes (see the “Methods” section). The red arrow indicates the Muc T type strain. B Within- and between-subspecies core-gene nucleotide identities confirm the subspecies diversification defined on the phylogeny. C Per-host frequency of A. muciniphila subspecies assembled from metagenomes. All 174 mouse A. muciniphila genomes were reconstructed from stool metagenomes of laboratory mice

Article Snippet: However, experimental Akkermansia research still heavily relies on the type strain A. muciniphila Muc T (ATCC BAA-835) and on a few more genomes of newly isolated strains that became available recently [ – ].

Techniques:

Journal: Genome Biology

Article Title: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

doi: 10.1186/s13059-021-02427-7

Figure Lengend Snippet: Summary of the number of genomes per candidate species

Article Snippet: However, experimental Akkermansia research still heavily relies on the type strain A. muciniphila Muc T (ATCC BAA-835) and on a few more genomes of newly isolated strains that became available recently [ – ].

Techniques: Generated

Journal: Microorganisms

Article Title: Akkermansia muciniphila and Faecalibacterium prausnitzii in Immune-Related Diseases

doi: 10.3390/microorganisms10122382

Figure Lengend Snippet: Characteristics of A. muciniphila and F. prausnitzii .

Article Snippet: In the guts of both humans and animals, Derrien et al. discovered the Verrucomicrobia phylum member A. muciniphila (type strain Muc T ; ATCC BAA-835).

Techniques: Permeability

Journal: BMJ Open

Article Title: Randomised double-blind placebo-controlled trial protocol to evaluate the therapeutic efficacy of lyophilised faecal microbiota capsules amended with next-generation beneficial bacteria in individuals with metabolic dysfunction-associated steatohepatitis

doi: 10.1136/bmjopen-2024-088290

Figure Lengend Snippet: Trophic chain converting fructo-oligosaccharides to butyrate through B. animalis subsp . lactis and A. soehngenii subsequently.

Article Snippet: Simultaneously, participants will daily ingest the capsules with doses of 10 9 A. soehngenii CH-106 cells (Caelus Health, Amsterdam, the Netherlands; dosage based on previous studies, including a toxicology study), 10 10 B. animalis subsp. lactis BLC1 cells (SynbioTec, Camerino, Italy) and 3×10 10 cells of pasteurised A. muciniphila strain Muc T (dosage based on European Food Safety Administration (EFSA) approval and obtained from the Akkermansia Company, Mont-Saint-Guibert, Belgium) for the entire 24 weeks.

Techniques: