1.Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).PubMed
Google Scholar
2.Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019).CAS
PubMed
PubMed Central
Google Scholar
3.Mohammad, B. F. et al. Structure and function of the global topsoil microbiome. Nature 560 233–237 (2018).4.Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).CAS
PubMed
PubMed Central
Google Scholar
5.Xiao, L. et al. A catalog of the mouse gut metagenome. Nat. Biotechnol. 33, 1103–1108 (2015).CAS
PubMed
Google Scholar
6.Coelho, L. P. et al. Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome 6, 72 (2018).PubMed
PubMed Central
Google Scholar
7.Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662.e20 (2019).CAS
PubMed
PubMed Central
Google Scholar
8.Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, (2018).9.Mende, D. R. et al. ProGenomes2: An improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Res. 48, D621–D625 (2020).CAS
PubMed
Google Scholar
10.Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).ADS
PubMed
PubMed Central
Google Scholar
11.Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).CAS
PubMed
PubMed Central
Google Scholar
12.Daniel H. et al. RefSeq: an update on prokaryotic genome annotation and curation. Nuc. Acids Res. 46, D851–D860 (2018).13.Mering, C. von et al. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315, 1126–1130 (2007).ADS
Google Scholar
14.Richardson, E. J. et al. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat. Ecol. Evol. 2, 1468–1478 (2018).PubMed
PubMed Central
Google Scholar
15.Nielsen, H. B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32, 822–828 (2014).CAS
PubMed
Google Scholar
16.Mende, D. R., Sunagawa, S., Zeller, G. & Bork, P. Accurate and universal delineation of prokaryotic species. Nat. Methods 10, 881–884 (2013).CAS
PubMed
Google Scholar
17.Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).CAS
PubMed
PubMed Central
Google Scholar
18.Louca, S. et al. Function and functional redundancy in microbial systems. Nat. Ecol. Evol. 2, 936–943 (2018).PubMed
Google Scholar
19.Maistrenko, O. M. et al. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. ISME J. 14, 1247–1259 (2020).PubMed
PubMed Central
Google Scholar
20.Baumdicker, F., Hess, W. R. & Pfaffelhuber, P. The diversity of a distributed genome in bacterial populations. Ann. Appl. Probab. 20, 1567–1606 (2010).MathSciNet
MATH
Google Scholar
21.Sela, I., Wolf, Y. I. & Koonin, E. V. Theory of prokaryotic genome evolution. Proc. Natl Acad. Sci. USA 113, 11399–11407 (2016).CAS
PubMed
PubMed Central
Google Scholar
22.Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324–328 (1998).CAS
PubMed
Google Scholar
23.Nei, M., Suzuki, Y. & Nozawa, M. The neutral theory of molecular evolution in the genomic era. Annu. Rev. Genomics Hum. Genet. 11, 265–289 (2010).CAS
PubMed
Google Scholar
24.Iranzo, J., Cuesta, J. A., Manrubia, S., Katsnelson, M. I. & Koonin, E. V. Disentangling the effects of selection and loss bias on gene dynamics. Proc. Natl Acad. Sci. USA 114, E5616–E5624 (2017).CAS
PubMed
PubMed Central
Google Scholar
25.Wolf, Y. I., Makarova, K. S., Lobkovsky, A. E. & Koonin, E. V. Two fundamentally different classes of microbial genes. Nat. Microbiol. 2, 16208 (2016).CAS
PubMed
Google Scholar
26.Rasko, D. A. et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol. 190, 6881–6893 (2008).CAS
PubMed
PubMed Central
Google Scholar
27.Koskella, B., Hall, L. J. & Metcalf, C. J. E. The microbiome beyond the horizon of ecological and evolutionary theory. Nat. Ecol. Evol. 1, 1606–1615 (2017).PubMed
Google Scholar
28.Liu, R. et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat. Med. 23, 859–868 (2017).CAS
PubMed
Google Scholar
29.Metcalf, J. L. et al. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 351, 158–162 (2015).ADS
PubMed
Google Scholar
30.Vincent, C. et al. Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection. Microbiome 4, 12 (2016).PubMed
PubMed Central
Google Scholar
31.Zeller, G. et al. Potential of fecal microbiota for early‐stage detection of colorectal cancer. Mol. Syst. Biol. 10, 766 (2014).PubMed
PubMed Central
Google Scholar
32.Gibson, M. K. et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat. Microbiol. 1, 16024 (2016).CAS
PubMed
PubMed Central
Google Scholar
33.Zhang, X. et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat. Med. 21, 895–905 (2015).CAS
PubMed
Google Scholar
34.Brito, I. L. et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 535, 435–439 (2016).ADS
CAS
PubMed
PubMed Central
Google Scholar
35.Vatanen, T. et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842–853 (2016).CAS
PubMed
PubMed Central
Google Scholar
36.Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804–810 (2007).ADS
CAS
PubMed
PubMed Central
Google Scholar
37.Hannigan, G. D. et al. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio 6, e01578-15 (2015).PubMed
PubMed Central
Google Scholar
38.Taft, D. H. et al. Intestinal microbiota of preterm infants differ over time and between hospitals. Microbiome 2, 36 (2014).PubMed
PubMed Central
Google Scholar
39.Zeevi, D. et al. Personalized nutrition by prediction of glycemic responses. Cell 163, 1079–1094 (2015).CAS
PubMed
Google Scholar
40.Wilhelm, R. C. et al. Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities. ISME J. 11, 2552–2568 (2017).PubMed
PubMed Central
Google Scholar
41.Xie, H. et al. Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome. Cell Syst. 3, 572–584.e3 (2016).CAS
PubMed
PubMed Central
Google Scholar
42.The MetaSUB International Consortium. The metagenomics and metadesign of the subways and urban biomes (metasub) international consortium inaugural meeting report. Microbiome 4, 24 (2016).
Google Scholar
43.Chatelier, E. L. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013).PubMed
Google Scholar
44.Li, J. et al. Gut microbiota dysbiosis contributes to the development of hypertension. Microbiome 5, (2017).45.Pehrsson, E. C. et al. Interconnected microbiomes and resistomes in low-income human habitats. Nature 533, 212–216 (2016).ADS
CAS
PubMed
PubMed Central
Google Scholar
46.Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 (2014).CAS
PubMed
Google Scholar
47.Feng, Q. et al. Gut microbiome development along the colorectal adenoma–carcinoma sequence. Nat. Commun. 6, 6528 (2015).ADS
CAS
PubMed
Google Scholar
48.Gu, Y. et al. Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment. Nat. Commun. 8, 1785 (2017).ADS
PubMed
PubMed Central
Google Scholar
49.Karlsson, F. H. et al. Gut metagenome in european women with normal, impaired and diabetic glucose control. Nature 498, 99–103 (2013).ADS
CAS
PubMed
Google Scholar
50.Yu, J. et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut 66, 70–78 (2017).CAS
PubMed
Google Scholar
51.Youngster, I. et al. Fecal microbiota transplant for relapsing clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study. Clin. Infect. Dis. 58, 1515–1522 (2014).PubMed
PubMed Central
Google Scholar
52.Guittar, J., Shade, A. & Litchman, E. Trait-based community assembly and succession of the infant gut microbiome. Nat. Commun. 10, 512 (2019).ADS
CAS
PubMed
PubMed Central
Google Scholar
53.Vogtmann, E. et al. Colorectal cancer and the human gut microbiome: reproducibility with whole-genome shotgun sequencing. PLoS ONE 11, e0155362 (2016).PubMed
PubMed Central
Google Scholar
54.Chng, K. R. et al. Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare. Nat Microbiol 1, 16106 (2016).CAS
PubMed
Google Scholar
55.Chu, D. M. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med. 23, 314–326 (2017).CAS
PubMed
PubMed Central
Google Scholar
56.Van Rossum, T. et al. Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes. Preprint at https://doi.org/10.1101/259861 (2018).57.Feng, Q. et al. Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. Sci. Rep. 6, 22525 (2016).ADS
CAS
PubMed
PubMed Central
Google Scholar
58.Oh, J., Byrd, A. L., Park, M., Kong, H. H. & Segre, J. A. Temporal stability of the human skin microbiome. Cell 165, 854–866 (2016).CAS
PubMed
PubMed Central
Google Scholar
59.Xiao, L. et al. A reference gene catalogue of the pig gut microbiome. Nat. Microbiol. 1, 16161 (2016).CAS
PubMed
Google Scholar
60.R Core Team. R: a language and environment for statistical computing (R Foundation for Statistical Computing, 2014).61.Coelho, L. P. et al. NG-meta-profiler: Fast processing of metagenomes using ngless, a domain-specific language. Microbiome 7, 84 (2019).PubMed
PubMed Central
Google Scholar
62.Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct De Bruijn graph. Bioinformatics 31, 1674–1676 (2015).CAS
PubMed
PubMed Central
Google Scholar
63.Besemer, J. & Borodovsky, M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33, W451–W454 (2005).CAS
PubMed
PubMed Central
Google Scholar
64.Coelho, L. P. Jug: Software for parallel reproducible computation in Python. J. Open Res. Softw. 5, 30 (2017).
Google Scholar
65.Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using diamond. Nat. Methods 12, 59–60 (2015).CAS
PubMed
Google Scholar
66.Eberhardt, R. Y. et al. AntiFam: A tool to help identify spurious ORFs in protein annotation. Database 2012, bas003 (2012).PubMed
PubMed Central
Google Scholar
67.Kang, D. et al. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).PubMed
PubMed Central
Google Scholar
68.Li, H. Aligning sequence reads, clone sequences and assembly contigs with bwa-mem. Preprint at https://arxiv.org/abs/1303.3997 (2013).69.Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).CAS
PubMed
PubMed Central
Google Scholar
70.Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).CAS
PubMed
PubMed Central
Google Scholar
71.Zhou, W., Gay, N. & Oh, J. ReprDB and panDB: minimalist databases with maximal microbial representation. Microbiome 6, 15 (2018).PubMed
PubMed Central
Google Scholar
72.Hingamp, P. et al. Exploring nucleo-cytoplasmic large DNA viruses in tara oceans microbial metagenomes. ISME J. 7, 1678–1695 (2013).CAS
PubMed
PubMed Central
Google Scholar
73.Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).CAS
PubMed
Google Scholar
74.Huerta-Cepas, J. et al. eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).CAS
PubMed
Google Scholar
75.Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).ADS
MathSciNet
CAS
PubMed
PubMed Central
Google Scholar
76.Smyshlyaev, G., Barabas, O. & Bateman, A. Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes. Mol. Syst. Biol. 17, e9880 (2021).CAS
PubMed
PubMed Central
Google Scholar
77.Jia, B. et al. CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573 (2017).CAS
PubMed
Google Scholar
78.Gibson, M. K., Forsberg, K. J. & Dantas, G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J. 9, 207–216 (2015).CAS
PubMed
Google Scholar
79.Li, T., Fan, K., Wang, J. & Wang, W. Reduction of protein sequence complexity by residue grouping. Protein Eng. 16, 323–330 (2003).CAS
PubMed
Google Scholar
80.Zhao, M., Lee, W.-P., Garrison, E. P. & Marth, G. T. SSW library: an SIMD Smith–Waterman C/C++ library for use in genomic applications. PLoS ONE 8, e82138 (2013).ADS
PubMed
PubMed Central
Google Scholar
81.Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2017).
Google Scholar
82.Milanese, A. et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nat. Commun. 10, 1014 (2019).ADS
PubMed
PubMed Central
Google Scholar
83.Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).PubMed
PubMed Central
Google Scholar
84.Kumar, R., Acharya, V., Singh, D. & Kumar, S. Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01. Stand. Genomic Sci. 13, 11 (2018).CAS
PubMed
PubMed Central
Google Scholar
85.Patijanasoontorn, B. et al. Hospital acquired Janthinobacterium lividum septicemia in srinagarind hospital. J. Med. Assoc. Thai. 75 Suppl 2, 6–10 (1992).PubMed
Google Scholar
86.Harris, C. R. et al. Array programming with NumPy. Nature 585, 357–362 (2020).ADS
CAS
PubMed
PubMed Central
Google Scholar
87.Virtanen, P. et al. SciPy 1.0: Fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).CAS
PubMed
PubMed Central
Google Scholar
88.Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).MathSciNet
MATH
Google Scholar
89.Collins, R. E. & Higgs, P. G. Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome. Mol. Biol. Evol. 29, 3413–3425 (2012).CAS
PubMed
Google Scholar
90.Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol. Syst. Biol. 7, 539 (2011).PubMed
PubMed Central
Google Scholar
91.Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).ADS
PubMed
PubMed Central
Google Scholar
92.Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016).CAS
PubMed
PubMed Central
Google Scholar
93.Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).CAS
PubMed
PubMed Central
Google Scholar
94.Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–12 (2006).CAS
PubMed
PubMed Central
Google Scholar
95.Murrell, B. et al. FUBAR: a fast, unconstrained Bayesian approximation for inferring selection. Mol. Biol. Evol. 30, 1196–1205 (2013).CAS
PubMed
PubMed Central
Google Scholar
96.Smith, M. D. et al. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol. Biol. Evol. 32, 1342–1353 (2015).CAS
PubMed
PubMed Central
Google Scholar
97.Washietl, S. et al. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA 17, 578–594 (2011).CAS
PubMed
PubMed Central
Google Scholar More