Page 23 - Read Online

Mueller et al. Microbiome Res Rep 2024;3:33 https://dx.doi.org/10.20517/mrr.2024.09 Page 17 of 18

19. Guo X, Li S, Zhang J, et al. Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and
functional diverisity, and global distribution in mammalian gut microbiotas. BMC Genomics 2017;18:800. DOI PubMed PMC
20. Becken B, Davey L, Middleton DR, et al. Genotypic and phenotypic diversity among human isolates of Akkermansia muciniphila.
mBio 2021;12:e00478-21. DOI PubMed PMC
21. Kelly C, Jawahar J, Davey L, et al. Spontaneous episodic inflammation in the intestines of mice lacking HNF4A is driven by
microbiota and associated with early life microbiota alterations. mBio 2023;14:e0150423. DOI PubMed PMC
22. Kirmiz N, Galindo K, Cross KL, et al. Comparative genomics guides elucidation of vitamin B biosynthesis in novel human-
12
associated akkermansia strains. Appl Environ Microbiol 2020;86:e02117-19. DOI PubMed PMC
23. Padilla L, Fricker AD, Luna E, et al. Mechanism of 2’-fucosyllactose degradation by human-associated Akkermansia. J Bacteriol
2024;206:e0033423. DOI PubMed PMC
24. Xing J, Li X, Sun Y, et al. Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species.
Genes Genomics 2019;41:1253-64. DOI PubMed PMC
25. Karcher N, Nigro E, Punčochář M, et al. Genomic diversity and ecology of human-associated Akkermansia species in the gut
microbiome revealed by extensive metagenomic assembly. Genome Biol 2021;22:209. DOI PubMed PMC
26. Kim JS, Kang SW, Lee JH, Park SH, Lee JS. The evolution and competitive strategies of Akkermansia muciniphila in gut. Gut
Microbes 2022;14:2025017. DOI PubMed PMC
27. Li W, Sun J, Jing Y, et al. Comparative genomics revealed wide intra-species genetic heterogeneity and lineage-specific genes of
Akkermansia muciniphila. Microbiol Spectr 2022;10:e0243921. DOI PubMed PMC
28. Bukhari SAR, Irfan M, Ahmad I, Chen L. Comparative genomics and pan-genome driven prediction of a reduced genome of
Akkermansia muciniphila. Microorganisms 2022;10:1350. DOI PubMed PMC
29. Kobayashi Y, Kawahara T, Inoue S, Kohda N. Akkermansia biwaensis sp. nov., an anaerobic mucin-degrading bacterium isolated from
human faeces. Int J Syst Evol Microbiol 2023;73:005697. DOI PubMed
30. Ndongo S, Armstrong N, Raoult D, Fournier PE. Reclassification of eight Akkermansia muciniphila strains and description of
Akkermansia massiliensis sp. nov. and Candidatus Akkermansia timonensis, isolated from human feces. Sci Rep 2022;12:21747. DOI
PubMed PMC
31. Zhai R, Xue X, Zhang L, Yang X, Zhao L, Zhang C. Strain-specific anti-inflammatory properties of two Akkermansia muciniphila
strains on chronic colitis in mice. Front Cell Infect Microbiol 2019;9:239. DOI PubMed PMC
32. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based
tools. Nucleic Acids Res 2013;41:D590-6. DOI PubMed PMC
33. McIver LJ, Abu-Ali G, Franzosa EA, et al. bioBakery: a meta’omic analysis environment. Bioinformatics 2018;34:1235-7. DOI
PubMed PMC
34. Oxford Nanopore Technologies. FAQs. Available from: https://nanoporetech.com/support. [Last accessed on 6 Jun 2024].
35. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019;37:540-6.
DOI PubMed
36. BCL convert. Illumina, Inc. Available from: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html. [Last
accessed on 6 Jun 2024].
37. Walker BJ, Abeel T, Shea T, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly
improvement. PLoS One 2014;9:e112963. DOI PubMed PMC
38. Gillespie JJ, Wattam AR, Cammer SA, et al. PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human
pathogenic species. Infect Immun 2011;79:4286-98. DOI PubMed PMC
39. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS
One 2013;8:e61217. DOI PubMed PMC
40. McCann JR, Bihlmeyer NA, Roche K, et al. The pediatric obesity microbiome and metabolism study (POMMS): methods, baseline
data, and early insights. Obesity 2021;29:569-78. DOI PubMed PMC
41. Derosa L, Routy B, Thomas AM, et al. Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with
advanced non-small-cell lung cancer. Nat Med 2022;28:315-24. DOI PubMed PMC
42. Mills RH, Dulai PS, Vázquez-Baeza Y, et al. Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus
proteases with disease severity. Nat Microbiol 2022;7:262-76. DOI PubMed PMC
43. Lloyd-Price J, Arze C, Ananthakrishnan AN, et al; IBDMDB Investigators. Multi-omics of the gut microbial ecosystem in
inflammatory bowel diseases. Nature 2019;569:655-62. DOI PubMed PMC
44. Franzosa EA, Sirota-Madi A, Avila-Pacheco J, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Nat Microbiol 2019;4:293-305. DOI PubMed PMC
45. Eren AM, Kiefl E, Shaiber A, et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 2021;6:3-6. DOI
PubMed PMC
46. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011;7:e1002195. DOI PubMed PMC
47. Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 2018;6:e4320. DOI
PubMed PMC
48. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting
enterobacterial plant pathogens. Anal Methods 2016;8:12-24. DOI