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Title: Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains

Abstract

Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a “next-generation probiotic.” However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitaminmore » B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome.« less

Authors:
 [1];  [1];  [2];  [1];  [3]; ORCiD logo [2]; ORCiD logo [1]
  1. California State Univ., Northridge, CA (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  3. California State Univ., Northridge, CA (United States); Univ. of California, Irvine, CA (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1606768
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 86; Journal Issue: 3; Journal ID: ISSN 0099-2240
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Akkermansia; human gut microbiome; intestinal bacteria; probiotics; vitamin B12

Citation Formats

Kirmiz, Nina, Galindo, Kadir, Cross, Karissa L., Luna, Estefani, Rhodes, Nicholas, Podar, Mircea, and Flores, Gilberto E. Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains. United States: N. p., 2019. Web. https://doi.org/10.1128/AEM.02117-19.
Kirmiz, Nina, Galindo, Kadir, Cross, Karissa L., Luna, Estefani, Rhodes, Nicholas, Podar, Mircea, & Flores, Gilberto E. Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains. United States. https://doi.org/10.1128/AEM.02117-19
Kirmiz, Nina, Galindo, Kadir, Cross, Karissa L., Luna, Estefani, Rhodes, Nicholas, Podar, Mircea, and Flores, Gilberto E. Fri . "Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains". United States. https://doi.org/10.1128/AEM.02117-19. https://www.osti.gov/servlets/purl/1606768.
@article{osti_1606768,
title = {Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains},
author = {Kirmiz, Nina and Galindo, Kadir and Cross, Karissa L. and Luna, Estefani and Rhodes, Nicholas and Podar, Mircea and Flores, Gilberto E.},
abstractNote = {Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a “next-generation probiotic.” However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome.},
doi = {10.1128/AEM.02117-19},
journal = {Applied and Environmental Microbiology},
number = 3,
volume = 86,
place = {United States},
year = {2019},
month = {11}
}

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Works referenced in this record:

Anvi’o: an advanced analysis and visualization platform for ‘omics data
journal, January 2015

  • Eren, A. Murat; Esen, Özcan C.; Quince, Christopher
  • PeerJ, Vol. 3
  • DOI: 10.7717/peerj.1319

The Mucin Degrader Akkermansia muciniphila Is an Abundant Resident of the Human Intestinal Tract
journal, December 2007

  • Derrien, M.; Collado, M. C.; Ben-Amor, K.
  • Applied and Environmental Microbiology, Vol. 74, Issue 5
  • DOI: 10.1128/AEM.01226-07

Akkermansia muciniphila induces gut microbiota remodelling and controls islet autoimmunity in NOD mice
journal, December 2017


Bacterial Community Variation in Human Body Habitats Across Space and Time
journal, November 2009


Shifting the genomic gold standard for the prokaryotic species definition
journal, October 2009

  • Richter, Michael; Rosselló-Móra, Ramon
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
  • DOI: 10.1073/pnas.0906412106

Quality control and preprocessing of metagenomic datasets
journal, January 2011


Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
journal, February 2014

  • Kim, M.; Oh, H. -S.; Park, S. -C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2
  • DOI: 10.1099/ijs.0.059774-0

Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila
journal, September 2017


Microbiota-Produced Succinate Improves Glucose Homeostasis via Intestinal Gluconeogenesis
journal, July 2016

  • De Vadder, Filipe; Kovatcheva-Datchary, Petia; Zitoun, Carine
  • Cell Metabolism, Vol. 24, Issue 1
  • DOI: 10.1016/j.cmet.2016.06.013

Investigating Deep Phylogenetic Relationships among Cyanobacteria and Plastids by Small Subunit rRNA Sequence Analysis
journal, July 1999


CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994

  • Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
  • Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
  • DOI: 10.1093/nar/22.22.4673

Detection of Succinate by Intestinal Tuft Cells Triggers a Type 2 Innate Immune Circuit
journal, July 2018


Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006

  • Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
  • Molecular Systems Biology, Vol. 2, Article No. 2006.0008
  • DOI: 10.1038/msb4100050

Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects
journal, September 2018

  • Lopez-Siles, Mireia; Enrich-Capó, Núria; Aldeguer, Xavier
  • Frontiers in Cellular and Infection Microbiology, Vol. 8
  • DOI: 10.3389/fcimb.2018.00281

Faecal levels of Bifidobacterium and Clostridium coccoides but not plasma lipopolysaccharide are inversely related to insulin and HOMA index in women
journal, December 2013

  • F. S. Teixeira, T.; Grześkowiak, Łukasz M.; Salminen, Seppo
  • Clinical Nutrition, Vol. 32, Issue 6
  • DOI: 10.1016/j.clnu.2013.02.008

Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites
journal, June 2016


Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens
journal, January 2016

  • Pritchard, Leighton; Glover, Rachel H.; Humphris, Sonia
  • Analytical Methods, Vol. 8, Issue 1
  • DOI: 10.1039/C5AY02550H

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria
journal, January 2010

  • Png, Chin Wen; Lindén, Sara K.; Gilshenan, Kristen S.
  • American Journal of Gastroenterology, Vol. 105, Issue 11
  • DOI: 10.1038/ajg.2010.281

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
journal, June 2010

  • Caporaso, J. G.; Lauber, C. L.; Walters, W. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1
  • DOI: 10.1073/pnas.1000080107

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011

  • Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1044

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015


Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics
journal, November 2018


Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission
journal, January 2013

  • Rajilić-Stojanović, Mirjana; Shanahan, Fergus; Guarner, Francisco
  • Inflammatory Bowel Diseases, Vol. 19, Issue 3
  • DOI: 10.1097/MIB.0b013e31827fec6d

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015

  • Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
  • Genome Research, Vol. 25, Issue 7
  • DOI: 10.1101/gr.186072.114

Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium
journal, September 2004

  • Derrien, M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 5
  • DOI: 10.1099/ijs.0.02873-0

Vitamin B 12 as a Modulator of Gut Microbial Ecology
journal, November 2014


Intestinal Integrity and Akkermansia muciniphila, a Mucin-Degrading Member of the Intestinal Microbiota Present in Infants, Adults, and the Elderly
journal, October 2007

  • Collado, M. C.; Derrien, M.; Isolauri, E.
  • Applied and Environmental Microbiology, Vol. 73, Issue 23
  • DOI: 10.1128/AEM.01477-07

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
journal, March 2013

  • Campbell, J. H.; O'Donoghue, P.; Campbell, A. G.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 14, p. 5540-5545
  • DOI: 10.1073/pnas.1303090110

Effect of Different Extraction Methods on Vitamin B12 from Blue Green Algae, Spirulina Platensis
journal, January 2015


Dietary Habits of 2- to 9-Year-Old American Children Are Associated with Gut Microbiome Composition
journal, April 2020

  • Herman, Dena R.; Rhoades, Nicholas; Mercado, Jasmine
  • Journal of the Academy of Nutrition and Dietetics, Vol. 120, Issue 4
  • DOI: 10.1016/j.jand.2019.07.024

Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function
journal, March 2017


Temporal variability is a personalized feature of the human microbiome
journal, December 2014

  • Flores, Gilberto E.; Caporaso, J. Gregory; Henley, Jessica B.
  • Genome Biology, Vol. 15, Issue 12
  • DOI: 10.1186/s13059-014-0531-y

Moving pictures of the human microbiome
journal, January 2011

  • Caporaso, J. Gregory; Lauber, Christian L.; Costello, Elizabeth K.
  • Genome Biology, Vol. 12, Issue 5
  • DOI: 10.1186/gb-2011-12-5-r50

Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014

  • Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1223

The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes
journal, March 2011


Isolation and Characterization of an H2-Oxidizing Thermophilic Methanogen
journal, January 1983


ARB: a software environment for sequence data
journal, February 2004


Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
journal, March 2011


SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

  • Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
  • Journal of Computational Biology, Vol. 19, Issue 5
  • DOI: 10.1089/cmb.2012.0021

The Microbiota of the Gut in Preschool Children With Normal and Excessive Body Weight
journal, November 2012

  • Karlsson, Caroline L. J.; Önnerfält, Jenny; Xu, Jie
  • Obesity, Vol. 20, Issue 11
  • DOI: 10.1038/oby.2012.110

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome
journal, January 2018


Tissue-specific transcriptomics and proteomics of a filarial nematode and its Wolbachia endosymbiont
journal, November 2015


Adaptation of Akkermansia muciniphila to the Oxic-Anoxic Interface of the Mucus Layer
journal, September 2016

  • Ouwerkerk, Janneke P.; van der Ark, Kees C. H.; Davids, Mark
  • Applied and Environmental Microbiology, Vol. 82, Issue 23
  • DOI: 10.1128/AEM.01641-16

ITEP: An integrated toolkit for exploration of microbial pan-genomes
journal, January 2014

  • Benedict, Matthew N.; Henriksen, James R.; Metcalf, William W.
  • BMC Genomics, Vol. 15, Issue 1
  • DOI: 10.1186/1471-2164-15-8

Short-chain fatty acids in control of energy metabolism
journal, June 2017


MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016

  • Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
  • Molecular Biology and Evolution, Vol. 33, Issue 7
  • DOI: 10.1093/molbev/msw054

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
journal, May 2013

  • Everard, A.; Belzer, C.; Geurts, L.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 22
  • DOI: 10.1073/pnas.1219451110

Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut
journal, January 2014


Effects of short chain fatty acids on gut morphology and function.
journal, January 1994


Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach
journal, February 2018

  • Chia, Loo Wee; Hornung, Bastian V. H.; Aalvink, Steven
  • Antonie van Leeuwenhoek, Vol. 111, Issue 6
  • DOI: 10.1007/s10482-018-1040-x

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
journal, June 2018

  • Rodriguez-R, Luis M.; Gunturu, Santosh; Harvey, William T.
  • Nucleic Acids Research, Vol. 46, Issue W1
  • DOI: 10.1093/nar/gky467

Library construction for next-generation sequencing: Overviews and challenges
journal, February 2014

  • Head, Steven R.; Komori, H. Kiyomi; LaMere, Sarah A.
  • BioTechniques, Vol. 56, Issue 2
  • DOI: 10.2144/000114133

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
journal, October 2018

  • Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky901

Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How?
journal, July 2018


Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle
journal, July 2017

  • Ottman, Noora; Davids, Mark; Suarez-Diez, Maria
  • Applied and Environmental Microbiology, Vol. 83, Issue 18
  • DOI: 10.1128/AEM.01014-17

Current IUBMB recommendations on enzyme nomenclature and kinetics
journal, May 2014


MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Microbes inside—from diversity to function: the case of Akkermansia
journal, March 2012


A next-generation beneficial microbe: Akkermansia muciniphila
journal, January 2018

  • Naito, Yuji; Uchiyama, Kazuhiko; Takagi, Tomohisa
  • Journal of Clinical Biochemistry and Nutrition, Vol. 63, Issue 1
  • DOI: 10.3164/jcbn.18-57

Dark chocolate as a stable carrier of microencapsulated Akkermansia muciniphila and Lactobacillus casei .
journal, December 2018

  • Marcial-Coba, Martín Sebastián; Saaby, Lasse; Knøchel, Susanne
  • FEMS Microbiology Letters, Vol. 366, Issue 2
  • DOI: 10.1093/femsle/fny290

Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine
journal, July 2016


A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice
journal, November 2016

  • Plovier, Hubert; Everard, Amandine; Druart, Céline
  • Nature Medicine, Vol. 23, Issue 1
  • DOI: 10.1038/nm.4236

Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces
journal, November 2016

  • Ouwerkerk, Janneke P.; Aalvink, Steven; Belzer, Clara
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 11
  • DOI: 10.1099/ijsem.0.001399

Akkermansia muciniphila and its role in regulating host functions
journal, May 2017


Cohabiting family members share microbiota with one another and with their dogs
journal, April 2013

  • Song, Se Jin; Lauber, Christian; Costello, Elizabeth K.
  • eLife, Vol. 2
  • DOI: 10.7554/eLife.00458