Page 24 - Read Online
P. 24
Page 18 of 18 Mueller et al. Microbiome Res Rep 2024;3:33 https://dx.doi.org/10.20517/mrr.2024.09
49. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol
Biol Evol 2009;26:1641-50. DOI PubMed PMC
50. Veseli I, Chen YT, Schechter MS, et al. Microbes with higher metabolic independence are enriched in human gut microbiomes under
stress. eLife 2023;12:RP89862. DOI
51. Sievers F, Wilm A, Dineen D, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal
Omega. Mol Syst Biol 2011;7:539. DOI PubMed PMC
52. RCoreTeam. The R project for statistical computing. Available from: https://www.r-project.org/. [Last accessed on 6 Jun 2024].
53. Beghini F, McIver LJ, Blanco-Míguez A, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial
communities with bioBakery 3. Elife 2021;10:e65088. DOI PubMed PMC
54. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from
metagenomes. Genome Res 2017;27:626-38. DOI PubMed PMC
55. Bisanz JE, Soto-Perez P, Noecker C, et al. A genomic toolkit for the mechanistic dissection of intractable human gut bacteria. Cell
Host Microbe 2020;27:1001-13.e9. DOI PubMed PMC
56. Emiola A, Zhou W, Oh J. Metagenomic growth rate inferences of strains in situ. Sci Adv 2020;6:eaaz2299. DOI PubMed PMC
57. Inkscape. Available from: https://inkscape.org/. [Last accessed on 6 Jun 2024].
58. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res
2021;49:W293-6. DOI PubMed PMC
59. GraphPad Prism. Available from: https://www.graphpad.com/. [Last accessed on 6 Jun 2024].
60. Luna E, Parkar SG, Kirmiz N, et al. Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain
dependent. Appl Environ Microbiol 2022;88:e0148721. DOI PubMed PMC
61. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their
relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81-91. DOI PubMed
62. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A
2009;106:19126-31. DOI PubMed PMC
63. Pearce ME, Langridge GC, Lauer AC, Grant K, Maiden MCJ, Chattaway MA. An evaluation of the species and subspecies of the
genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII, VIII,
IX, X and XI. Genomics 2021;113:3152-62. DOI PubMed PMC
64. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence
similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346-51. DOI PubMed
65. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present
species definition in bacteriology. Int J Syst Evol Microbiol 1994;44:846-9. DOI
66. Lv QB, Li S, Zhang Y, et al. A thousand metagenome-assembled genomes of Akkermansia reveal phylogroups and geographical and
functional variations in the human gut. Front Cell Infect Microbiol 2022;12:957439. DOI PubMed PMC
67. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic
purposes. Int J Syst Evol Microbiol 2010;60:249-66. DOI PubMed
68. Diogo A, Veríssimo A, Nobre MF, da Costa MS. Usefulness of fatty acid composition for differentiation of Legionella species. J Clin
Microbiol 1999;37:2248-54. DOI PubMed PMC
69. Hall AB, Yassour M, Sauk J, et al. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome
Med 2017;9:103. DOI PubMed PMC
70. Rice P, Longden I, Bleasby A. EMBOSS: the european molecular biology open software suite. Trends Genet 2000;16:276-7. DOI
PubMed
71. Choi Y, Bose S, Seo J, et al. Effects of live and pasteurized forms of akkermansia from the human gut on obesity and metabolic
dysregulation. Microorganisms 2021;9:2039. DOI PubMed PMC
72. Zhang T, Li P, Wu X, et al. Alterations of Akkermansia muciniphila in the inflammatory bowel disease patients with washed
microbiota transplantation. Appl Microbiol Biotechnol 2020;104:10203-15. DOI PubMed
73. Lopez-Siles M, Enrich-Capó N, Aldeguer X, et al. Alterations in the abundance and co-occurrence of Akkermansia muciniphila and
Faecalibacterium prausnitzii in the colonic mucosa of inflammatory bowel disease subjects. Front Cell Infect Microbiol 2018;8:281.
DOI PubMed PMC
74. Shaw KA, Bertha M, Hofmekler T, et al. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects
with newly diagnosed inflammatory bowel disease. Genome Med 2016;8:75. DOI PubMed PMC
75. Jin Y, Zhou J, Zhou J, et al. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic
status. Biol Direct 2020;15:6. DOI PubMed PMC
76. Caudill MT, Brayton KA. The use and limitations of the 16S rRNA sequence for species classification of anaplasma samples.
Microorganisms 2022;10:605. DOI PubMed PMC
77. González D, Morales-Olavarria M, Vidal-Veuthey B, Cárdenas JP. Insights into early evolutionary adaptations of the Akkermansia
genus to the vertebrate gut. Front Microbiol 2023;14:1238580. DOI PubMed PMC

