in

Trait biases in microbial reference genomes

  • Overmann, J., Abt, B. & Sikorski, J. Present and future of culturing bacteria. Annual Review of Microbiology 71, 711–730 (2017).

    CAS 

    Google Scholar 

  • O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research 44, D733 (2016).

    Google Scholar 

  • Bobay, L. M. & Ochman, H. Biological species are universal across life’s domains. Genome Biology and Evolution 9, 491–501 (2017).

    Google Scholar 

  • Magnabosco, C., Moore, K., Wolfe, J. & Fournier, G. Dating phototrophic microbial lineages with reticulate gene histories. Geobiology 16, 179–189 (2018).

    CAS 

    Google Scholar 

  • Louca, S. et al. Function and functional redundancy in microbial systems. Nature Ecology & Evolution 2, 936–943 (2018).

    ADS 

    Google Scholar 

  • Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90 K prokaryotic genomes reveals clear species boundaries. Nature Communications 9, 5114 (2018).

    ADS 

    Google Scholar 

  • Zhu, Q. et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains bacteria and archaea. Nature Communications 10, 5477 (2019).

    ADS 
    CAS 

    Google Scholar 

  • Royalty, T.M. & Steen, A.D. Quantitatively partitioning microbial genomic traits among taxonomic ranks across the microbial tree of life. mSphere 4 (2019).

  • Murray, C. S., Gao, Y. & Wu, M. Re-evaluating the evidence for a universal genetic boundary among microbial species. Nature Communications 12, 4059 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research 42, D231–D239 (2014).

    CAS 

    Google Scholar 

  • Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. & Schmidt, T. M. rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Research 43, D593–D598 (2014).

    Google Scholar 

  • Douglas, G. M. et al. Picrust2 for prediction of metagenome functions. Nature Biotechnology 38, 685–688 (2020).

    CAS 

    Google Scholar 

  • Wemheuer, F. et al. Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environmental Microbiome 15, 1–12 (2020).

    Google Scholar 

  • Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).

    ADS 
    CAS 

    Google Scholar 

  • Wu, D. et al. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462, 1056–1060 (2009).

    ADS 
    CAS 

    Google Scholar 

  • Louca, S. & Pennell, M. W. A general and efficient algorithm for the likelihood of diversification and discrete-trait evolutionary models. Systematic Biology 69, 545–556 (2020).

    Google Scholar 

  • Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004).

    ADS 
    CAS 

    Google Scholar 

  • Sharon, I. & Banfield, J. F. Genomes from metagenomics. Science 342, 1057–1058 (2013).

    ADS 
    CAS 

    Google Scholar 

  • Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology 2, 1533–1542 (2017).

    CAS 

    Google Scholar 

  • Chen, L. X., Anantharaman, K., Shaiber, A., Eren, A. M. & Banfield, J. F. Accurate and complete genomes from metagenomes. Genome Research 30, 315–333 (2020).

    CAS 

    Google Scholar 

  • Konstantinidis, K. T. & Tiedje, J. M. Genomic insights that advance the species definition for prokaryotes. Proceedings of the National Academy of Sciences 102, 2567–2572 (2005).

    ADS 
    CAS 

    Google Scholar 

  • Kim, M., Oh, H. S., Park, S. C. & Chun, J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Journal of Systematic and Evolutionary Microbiology 64, 346–351 (2014).

    CAS 

    Google Scholar 

  • Shapiro, B.J. What microbial population genomics has taught us about speciation. In Polz, M.F. & Rajora, O.P. (eds.) Population Genomics: Microorganisms, 31–47 (Springer International Publishing, Cham, Switzerland, 2019).

  • Olm, M. R. et al. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems 5, e00731–19 (2020).

    CAS 

    Google Scholar 

  • Lagkouvardos, I., Overmann, J. & Clavel, T. Cultured microbes represent a substantial fraction of the human and mouse gut microbiota. Gut Microbes 8, 493–503 (2017).

    Google Scholar 

  • Zhang, Z., Wang, J., Wang, J., Wang, J. & Li, Y. Estimate of the sequenced proportion of the global prokaryotic genome. Microbiome 8, 1–9 (2020).

    Google Scholar 

  • Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2019).

    Google Scholar 

  • Mira, A., Ochman, H. & Moran, N. A. Deletional bias and the evolution of bacterial genomes. Trends in Genetics 17, 589–596 (2001).

    CAS 

    Google Scholar 

  • Morris, J. J., Lenski, R. E. & Zinser, E. R. The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. MBio 3, e00036–12 (2012).

    Google Scholar 

  • Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME Journal 8, 1553–1565 (2014).

    Google Scholar 

  • Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).

    ADS 
    CAS 

    Google Scholar 

  • Gary, P.R. Adjusting for nonresponse in surveys. In Smart, J.C. (ed.) Higher Education: Handbook of Theory and Research, chap. 8, 411–449 (Springer, Dordrecht, Netherlands, 2007).

  • Maguire, F. et al. Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic islands. Microbial Genomics 6, mgen000436 (2020).

    Google Scholar 

  • 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 Research 47, D309–D314 (2019).

    CAS 

    Google Scholar 

  • Abdel-Hamid, A.M., Solbiati, J.O., Cann, I.K.O., Sariaslani, S. & Gadd, G.M. Insights into lignin degradation and its potential industrial applications, vol. 82, chap. 1, 1–28 (Academic Press, 2013).

  • El-Bondkly, A.M. Sequence analysis of industrially important genes from trichoderma. In Biotechnology and biology of Trichoderma, chap. 28, 377–392 (Elsevier, 2014).

  • Dawood, A. & Ma, K. Applications of microbial β-mannanases. Frontiers in Bioengineering and Biotechnology 8 (2020).

  • Khelaifia, S., Raoult, D. & Drancourt, M. A versatile medium for cultivating methanogenic archaea. PLOS ONE 8, e61563 (2013).

    ADS 
    CAS 

    Google Scholar 

  • Khelaifia, S. et al. Aerobic culture of methanogenic archaea without an external source of hydrogen. European Journal of Clinical Microbiology & Infectious Diseases 35, 985–991 (2016).

    CAS 

    Google Scholar 

  • Michał, B. et al. Phymet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens. Environmental Microbiology Reports 10, 378–382 (2018).

    Google Scholar 

  • Albright, S. & Louca, S. Trait biases in microbial reference genomes, figshare., https://doi.org/10.6084/m9.figshare.c.6055004.v1 (2022).

  • Castelle, C. J. & Banfield, J. F. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172, 1181–1197 (2018).

    CAS 

    Google Scholar 

  • Murray, A. E. et al. Roadmap for naming uncultivated archaea and bacteria. Nature Microbiology 5, 987–994 (2020).

    CAS 

    Google Scholar 

  • Palleroni, N. J. Prokaryotic diversity and the importance of culturing. Antonie van Leeuwenhoek 72, 3–19 (1997).

    CAS 

    Google Scholar 

  • Langille, M. G. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology 31, 814–821 (2013).

    CAS 

    Google Scholar 

  • Tran, P. Q. et al. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. The ISME Journal 15, 1971–1986 (2021).

    CAS 

    Google Scholar 

  • Kroeger, M. E. et al. New biological insights into how deforestation in amazonia affects soil microbial communities using metagenomics and metagenome-assembled genomes. Frontiers in Microbiology 9, 1635 (2018).

    Google Scholar 

  • Nathani, N. M. et al. 309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula. Scientific Data 8, 194 (2021).

    Google Scholar 

  • Irazoqui, J. M., Eberhardt, M. F., Adjad, M. M., Amadio, A. F. & Collado, M. C. Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics. PeerJ 10, e12772 (2022).

    Google Scholar 

  • Hwang, Y. et al. Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core. Microbiome 9, 234 (2021).

    CAS 

    Google Scholar 

  • Tully, B., Wheat, C. G., Glazer, B. T. & Huber, J. A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. ISME Journal 12, 1–16 (2018).

    CAS 

    Google Scholar 

  • Vanwonterghem, I., Jensen, P. D., Rabaey, K. & Tyson, G. W. Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environmental Microbiology 18, 3144–3158 (2016).

    CAS 

    Google Scholar 

  • Glasl, B. et al. Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. The ISME Journal 14, 1435–1450 (2020).

    Google Scholar 

  • Robbins, S. J. et al. A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology 4, 2090–2100 (2019).

    Google Scholar 

  • Engelberts, J. P. et al. Characterization of a sponge microbiome using an integrative genome-centric approach. The ISME Journal 14, 1100–1110 (2020).

    CAS 

    Google Scholar 

  • Bowerman, K. L. et al. Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nature Communications 11, 5886 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Chen, Y. J. et al. Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments. The ISME Journal 16, 750–763 (2022).

    CAS 

    Google Scholar 

  • Hugerth, L. W. et al. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biology 16, 279 (2015).

    Google Scholar 

  • Alneberg, J. et al. Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Communications Biology 3, 119 (2020).

    Google Scholar 

  • Di Cesare, A. et al. Genomic comparison and spatial distribution of different Synechococcus phylotypes in the Black Sea. Frontiers in Microbiology 11, 1979 (2020).

    Google Scholar 

  • van Vliet, D. M. et al. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environmental Microbiology 23, 2834–2857 (2021).

    Google Scholar 

  • Dalcin Martins, P. et al. Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments. MicrobiologyOpen 10, e1175 (2021).

    CAS 

    Google Scholar 

  • Stewart, R. D. et al. Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. Nature Biotechnology 37, 953–961 (2019).

    CAS 

    Google Scholar 

  • Segura-Wang, M., Grabner, N., Koestelbauer, A., Klose, V. & Ghanbari, M. Genome-resolved metagenomics of the chicken gut microbiome. Frontiers in Microbiology 12, 726923 (2021).

    Google Scholar 

  • Ruuskanen, M. O. et al. Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments. Limnology and Oceanography 65, S233–S247 (2020).

    CAS 

    Google Scholar 

  • Haas, S., Desai, D. K., LaRoche, J., Pawlowicz, R. & Wallace, D. W. R. Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater. Environmental Microbiology 21, 3927–3952 (2019).

    CAS 

    Google Scholar 

  • Spasov, E. et al. High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. The ISME Journal 14, 1857–1872 (2020).

    CAS 

    Google Scholar 

  • Vigneron, A. et al. Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem. Microbiome 9, 46 (2021).

    CAS 

    Google Scholar 

  • Galambos, D., Anderson, R. E., Reveillaud, J. & Huber, J. A. Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents. Environmental Microbiology 21, 4395–4410 (2019).

    CAS 

    Google Scholar 

  • Stewart, R. D. et al. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nature Communications 9, 870 (2018).

    ADS 

    Google Scholar 

  • Xing, P. et al. Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake. Limnology and Oceanography 65, S134–S148 (2020).

    Google Scholar 

  • Zhang, S., Hu, Z. & Wang, H. Metagenomic analysis exhibited the co-metabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment. Environment International 129, 308–319 (2019).

    CAS 

    Google Scholar 

  • Lin, Y., Wang, L., Xu, K., Li, K. & Ren, H. Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics. Microbiome 9, 67 (2021).

    CAS 

    Google Scholar 

  • Liu, L. et al. High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method. Microbiome 8, 155 (2020).

    CAS 

    Google Scholar 

  • Kantor, R. S. et al. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environmental Microbiology 17, 4929–4941 (2015).

    CAS 

    Google Scholar 

  • Zhou, Z. et al. Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. The ISME Journal 14, 3136–3148 (2020).

    CAS 

    Google Scholar 

  • Reysenbach, A. L. et al. Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities. Proceedings of the National Academy of Sciences 117, 32627–32638 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Hou, J. et al. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. Microbiome 8, 102 (2020).

    CAS 

    Google Scholar 

  • Campanaro, S. et al. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. Biotechnology for Biofuels 9, 26 (2016).

    Google Scholar 

  • Singleton, C. M. et al. Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing. Nature Communications 12, 2009 (2021).

    CAS 

    Google Scholar 

  • Diamond, S. et al. Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature Microbiology 4, 1356–1367 (2019).

    CAS 

    Google Scholar 

  • Rasigraf, O. et al. Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter. Limnology and Oceanography 65, S113–S133 (2020).

    CAS 

    Google Scholar 

  • Rissanen, A. J. et al. Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes. FEMS Microbiology Ecology 97, fiaa252 (2021).

    CAS 

    Google Scholar 

  • Campanaro, S. et al. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. Biotechnology for Biofuels 13, 25 (2020).

    CAS 

    Google Scholar 

  • Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology 39, 105–114 (2021).

    CAS 

    Google Scholar 

  • Zhou, Z. et al. Genome- and community-level interaction insights into carbon utilization and element cycling functions of hydrothermarchaeota in hydrothermal sediment. mSystems 5 (2020).

  • Pachiadaki, M. G. et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell 179, 1623–1635.e11 (2019).

    CAS 

    Google Scholar 

  • Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101–105 (2018).

    ADS 
    CAS 

    Google Scholar 

  • Greenlon, A. et al. Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proceedings of the National Academy of Sciences 116, 15200–15209 (2019).

    ADS 
    CAS 

    Google Scholar 

  • Hervé, V. et al. Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ 8, e8614 (2020).

    Google Scholar 

  • von Appen, W.J. The expedition PS114 of the research vessel POLARSTERN to the Fram Strait in 2018. Tech. Rep., Alfred Wegener Institute for Polar and Marine Research (2018).

  • Dombrowski, N., Seitz, K. W., Teske, A. P. & Baker, B. J. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments. Microbiome 5, 106 (2017).

    Google Scholar 

  • Yu, J. et al. Dna-stable isotope probing shotgun metagenomics reveals the resilience of active microbial communities to biochar amendment in oxisol soil. Frontiers in Microbiology 11, 587972 (2020).

    Google Scholar 

  • Forster, S. C. et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. Nature Biotechnology 37, 186–192 (2019).

    CAS 

    Google Scholar 

  • Gharechahi, J. et al. Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen. The ISME Journal 15, 1108–1120 (2021).

    CAS 

    Google Scholar 

  • Meier, D. V., Imminger, S., Gillor, O. & Woebken, D. Distribution of mixotrophy and desiccation survival mechanisms across microbial genomes in an arid biological soil crust community. mSystems 6, e00786–20 (2021).

    CAS 

    Google Scholar 

  • Haro-Moreno, J. M. et al. Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability. FEMS Microbiology Ecology 96, fiaa218 (2020).

    CAS 

    Google Scholar 

  • Haro-Moreno, J. M. et al. Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment. Microbiome 6, 128 (2018).

    Google Scholar 

  • Dong, X. et al. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nature Communications 10, 1816 (2019).

    ADS 

    Google Scholar 

  • Poghosyan, L. et al. Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters. Water Research 185, 116288 (2020).

    CAS 

    Google Scholar 

  • Paula, D. M., Jeroen, F., Hugh, M. & Meng, M. L. & J., W.M. Wetland sediments host diverse microbial taxa capable of cycling alcohols. Applied and Environmental Microbiology 85, 00189–19 (2019).

    Google Scholar 

  • Aromokeye, D. A. et al. Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures. The ISME Journal 15, 965–980 (2021).

    CAS 

    Google Scholar 

  • Borchert, E. et al. Deciphering a marine bone-degrading microbiome reveals a complex community effort. mSystems 6, e01218–20 (2021).

    CAS 

    Google Scholar 

  • Osvatic, J. T. et al. Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. Proceedings of the National Academy of Sciences 118, e2104378118 (2021).

    CAS 

    Google Scholar 

  • Boeuf, D. et al. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proceedings of the National Academy of Sciences 116, 11824–11832 (2019).

    ADS 
    CAS 

    Google Scholar 

  • Woodcroft, B. J. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018).

    ADS 
    CAS 

    Google Scholar 

  • Alqahtani, M. F. et al. Enrichment of Marinobacter sp. and halophilic homoacetogens at the biocathode of microbial electrosynthesis system inoculated with Red Sea brine pool. Frontiers in Microbiology 10, 2563 (2019).

    Google Scholar 

  • Haroon, M. F., Thompson, L. R., Parks, D. H., Hugenholtz, P. & Stingl, U. A catalogue of 136 microbial draft genomes from Red Sea metagenomes. Scientific Data 3, 160050 (2016).

    CAS 

    Google Scholar 

  • Vavourakis, C. D. et al. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome 6, 1–18 (2018).

    Google Scholar 

  • Cabello-Yeves, P. J. et al. Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat. Limnology and Oceanography 65, 1471–1488 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Vavourakis, C. D. et al. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a siberian soda lake. BMC Biology 17, 69 (2019).

    Google Scholar 

  • Waterworth, S. C., Isemonger, E. W., Rees, E. R., Dorrington, R. A. & Kwan, J. C. Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds. Environmental Microbiology Reports 13, 126–137 (2021).

    CAS 

    Google Scholar 

  • Huddy, R. J. et al. Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes. Frontiers in Microbiology 12, 643368 (2021).

    Google Scholar 

  • Emerson, J. B. et al. Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nature Communications 12, 5815 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Chiri, E. et al. Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds. Proceedings of the National Academy of Sciences 118, e2102625118 (2021).

    CAS 

    Google Scholar 

  • Gong, G., Zhou, S., Luo, R., Gesang, Z. & Suolang, S. Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community. BMC Microbiology 20, 302 (2020).

    Google Scholar 

  • Zhou, S. et al. Characterization of metagenome-assembled genomes and carbohydrate-degrading genes in the gut microbiota of Tibetan pig. Frontiers in Microbiology 11, 595066 (2020).

    Google Scholar 

  • Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Scientific Data 5, 170203 (2018).

    CAS 

    Google Scholar 

  • Lavrinienko, A. et al. Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota. Scientific Data 7, 312 (2020).

    CAS 

    Google Scholar 

  • Peng, X. et al. Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. Nature Microbiology 6, 499–511 (2021).

    CAS 

    Google Scholar 

  • Dudek, N. K. et al. Novel microbial diversity and functional potential in the marine mammal oral microbiome. Current Biology 27, 3752–3762.e6 (2017).

    CAS 

    Google Scholar 

  • Pinto, A. J. et al. Metagenomic evidence for the presence of comammox nitrospira-like bacteria in a drinking water system. mSphere 1, e00054–15 (2015).

    Google Scholar 

  • Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).

    ADS 
    CAS 

    Google Scholar 

  • Nobu, M. K. et al. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome 8, 111 (2020).

    CAS 

    Google Scholar 

  • Butterfield, C. N. et al. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 4, e2687 (2016).

    Google Scholar 

  • Castelle, C. J. et al. Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN Archaea. Frontiers in Microbiology 12, 660052 (2021).

    Google Scholar 

  • Alteio, L. V. et al. Complementary metagenomic approaches improve reconstruction of microbial diversity in a forest soil. mSystems 5, e00768–19 (2020).

    Google Scholar 

  • Shaiber, A. et al. Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biology 21, 292 (2020).

    Google Scholar 

  • Jungbluth, S. P., Amend, J. P. & Rappé, M. S. Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Scientific Data 4, 170037 (2017).

    CAS 

    Google Scholar 

  • Sheik, C. S. et al. Dolichospermum blooms in Lake Superior: DNA-based approach provides insight to the past, present and future of blooms. Journal of Great Lakes Research 48, 1191–1205 (2022).

    CAS 

    Google Scholar 

  • Barnum, T. P. et al. Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities. The ISME Journal 12, 1568–1581 (2018).

    CAS 

    Google Scholar 

  • Julian, D. et al. Coastal ocean metagenomes and curated metagenome-assembled genomes from Marsh Landing, Sapelo Island (Georgia, USA). Microbiology Resource Announcements 8, e00934–19 (2019).

    Google Scholar 

  • Breister, A. M. et al. Soil microbiomes mediate degradation of vinyl ester-based polymer composites. Communications Materials 1, 101 (2020).

    ADS 

    Google Scholar 

  • Fu, H., Uchimiya, M., Gore, J. & Moran, M. A. Ecological drivers of bacterial community assembly in synthetic phycospheres. Proceedings of the National Academy of Sciences 117, 3656–3662 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Nobu, M. K. et al. Thermodynamically diverse syntrophic aromatic compound catabolism. Environmental Microbiology 19, 4576–4586 (2017).

    CAS 

    Google Scholar 

  • 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 (2019).

    CAS 

    Google Scholar 

  • Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nature Biotechnology 39, 499–509 (2021).

    CAS 

    Google Scholar 

  • Li, Z. et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. The ISME Journal 15, 2366–2378 (2021).

    CAS 

    Google Scholar 

  • Bay, S. K. et al. Trace gas oxidizers are widespread and active members of soil microbial communities. Nature Microbiology 6, 246–256 (2021).

    CAS 

    Google Scholar 

  • Seyler, L. M., Trembath-Reichert, E., Tully, B. J. & Huber, J. A. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. The ISME Journal 15, 1192–1206 (2021).

    CAS 

    Google Scholar 

  • Herold, M. et al. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nature Communications 11, 5281 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Dong, X. et al. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nature Communications 11, 5825 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Thompson, L. R. et al. Metagenomic covariation along densely sampled environmental gradients in the Red Sea. The ISME Journal 11, 138–151 (2017).

    CAS 

    Google Scholar 

  • Dominik, S., Daniela, Z., Anja, P., Katharina, R. & Rolf, D. Metagenome-assembled genome sequences from different wastewater treatment stages in Germany. Microbiology Resource Announcements 10, e00504–21 (2021).

    Google Scholar 

  • Langwig, M. V. et al. Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. The ISME Journal 16, 307–320 (2022).

    CAS 

    Google Scholar 

  • Rezaei Somee, M. et al. Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents. Scientific Reports 11, 11316 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Gilroy, R. et al. Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity. PeerJ 10, e13084 (2022).

    Google Scholar 

  • Bhattarai, B., Bhattacharjee, A. S., Coutinho, F. H. & Goel, R. K. Viruses and their interactions with bacteria and archaea of hypersaline Great Salt Lake. Frontiers in Microbiology 12, 701414 (2021).

    Google Scholar 

  • Liu, L. et al. Microbial diversity and adaptive strategies in the Mars-like Qaidam Basin, North Tibetan Plateau, China. Environmental Microbiology Reports (2022).

  • Lin, H. et al. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The ISME Journal 15, 1810–1825 (2021).

    CAS 

    Google Scholar 

  • Martnez-Pérez, C. et al. Lifting the lid: nitrifying archaea sustain diverse microbial communities below the Ross Ice Shelf. SSRN (2020).

  • Zhang, L. et al. Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system. Science of The Total Environment 791, 148096 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Starr, E. P. et al. Stable-isotope-informed, genome-resolved metagenomics uncovers potential cross-kingdom interactions in rhizosphere soil. mSphere 6, e00085–21 (2021).

    CAS 

    Google Scholar 

  • Matthew, C. et al. Archaeal and bacterial metagenome-assembled genome sequences derived from pig feces. Microbiology Resource Announcements 11, 01142–21 (2022).

    Google Scholar 

  • Wang, Y., Zhao, R., Liu, L., Li, B. & Zhang, T. Selective enrichment of comammox from activated sludge using antibiotics. Water Research 197, 117087 (2021).

    CAS 

    Google Scholar 

  • Gilroy, R. et al. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ 9, e10941 (2021).

    Google Scholar 

  • Chen, Y. H. et al. Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach. Communications Biology 4, 996 (2021).

    CAS 

    Google Scholar 

  • Beach, N. K., Myers, K. S., Donohue, T. J. & Noguera, D. R. Metagenomes from 25 low-abundance microbes in a partial nitritation anammox microbiome. Microbiology Resource Announcements 11, 00212–22 (2022).

    CAS 

    Google Scholar 

  • Solanki, V. et al. Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi. The ISME Journal 16, 1818–1830 (2022).

    CAS 

    Google Scholar 

  • Hiraoka, S. et al. Diverse DNA modification in marine prokaryotic and viral communities. Nucleic Acids Research 50, 1531–1550 (2022).

    CAS 

    Google Scholar 

  • Haryono, M.A.S. et al. Recovery of high quality metagenome-assembled genomes from full-scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling. Frontiers in Microbiology 13 (2022).

  • Rodrguez-Ramos, J.A. et al. Microbial genome-resolved metaproteomic analyses frame intertwined carbon and nitrogen cycles in river hyporheic sediments. Research Square (2021).

  • Kim, M., Cho, H. & Lee, W. Y. Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica. Journal of Microbiology 58, 1018–1026 (2020).

    CAS 

    Google Scholar 

  • Voorhies, A. A. et al. Cyanobacterial life at low O2: community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat. Geobiology 10, 250–267 (2012).

    CAS 

    Google Scholar 

  • McDaniel, E. A. et al. Tbasco: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome. ISME Communications 2, 111 (2022).

    Google Scholar 

  • Wang, W. et al. Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary. AMB Express 10, 16 (2020).

    Google Scholar 

  • Mandakovic, D. et al. Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment. Scientific Reports 10, 5560 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Wang, Y. et al. Seasonal prevalence of ammonia-oxidizing archaea in a full-scale municipal wastewater treatment plant treating saline wastewater revealed by a 6-year time-series analysis. Environmental Science & Technology 55, 2662–2673 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Bulzu, P. A. et al. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nature Microbiology 4, 1129–1137 (2019).

    CAS 

    Google Scholar 

  • Karen, J. et al. Hydrogen-oxidizing bacteria are abundant in desert soils and strongly stimulated by hydration. mSystems 5, e01131–20 (2020).

    Google Scholar 

  • Rust, M. et al. A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli. Proceedings of the National Academy of Sciences 117, 9508–9518 (2020).

    ADS 
    CAS 

    Google Scholar 

  • Podowski, J. C., Paver, S. F., Newton, R. J. & Coleman, M. L. Genome streamlining, proteorhodopsin, and organic nitrogen metabolism in freshwater nitrifiers. mBio 13, e02379–21 (2022).

    Google Scholar 

  • Coutinho, F. H. et al. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. Microbiome 8, 163 (2020).

    CAS 

    Google Scholar 

  • Philippi, M. et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nature Communications 12, 4774 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Katie, S. et al. Eight metagenome-assembled genomes provide evidence for microbial adaptation in 20,000- to 1,000,000-year-old Siberian permafrost. Applied and Environmental Microbiology 87, e00972–21 (2021).

    Google Scholar 

  • Mert, K. et al. Unexpected abundance and diversity of phototrophs in mats from morphologically variable microbialites in Great Salt Lake, Utah. Applied and Environmental Microbiology 86, e00165–20 (2020).

    Google Scholar 

  • Patin, N. V. et al. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. The ISME Journal 15, 2206–2232 (2021).

    CAS 

    Google Scholar 

  • Wang, J., Tang, X., Mo, Z. & Mao, Y. Metagenome-assembled genomes from Pyropia haitanensis microbiome provide insights into the potential metabolic functions to the seaweed. Frontiers in Microbiology 13, 857901 (2022).

    Google Scholar 

  • Burgsdorf, I. et al. Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool. The ISME Journal 16, 1163–1175 (2022).

    CAS 

    Google Scholar 

  • Suarez, C. et al. Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms. npj Biofilms and Microbiomes 8, 47 (2022).

    CAS 

    Google Scholar 

  • Kumar, D. et al. Textile industry wastewaters from Jetpur, Gujarat, India, are dominated by Shewanellaceae, Bacteroidaceae, and Pseudomonadaceae harboring genes encoding catalytic enzymes for textile dye degradation. Frontiers in Environmental Science 9, 720707 (2021).

    ADS 

    Google Scholar 

  • Seitz, V. A. et al. Variation in root exudate composition influences soil microbiome membership and function. Applied and Environmental Microbiology 88, e00226–22 (2022).

    Google Scholar 

  • Lindner, B. G. et al. Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms. Water Research 210, 117993 (2022).

    CAS 

    Google Scholar 

  • Yancey, C. E. et al. Metagenomic and metatranscriptomic insights into population diversity of microcystis blooms: Spatial and temporal dynamics of mcy genotypes, including a partial operon that can be abundant and expressed. Applied and Environmental Microbiology 88, e02464–21 (2022).

    Google Scholar 

  • Liu, L. et al. Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy. Microbiome 9, 205 (2021).

    CAS 

    Google Scholar 

  • Speth, D. R. et al. Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily. The ISME Journal 16, 1750–1764 (2022).

    CAS 

    Google Scholar 

  • Blyton, M. D. J., Soo, R. M., Hugenholtz, P. & Moore, B. D. Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environmental Microbiology 24, 475–493 (2022).

    CAS 

    Google Scholar 

  • Nuccio, E. E. et al. Niche differentiation is spatially and temporally regulated in the rhizosphere. The ISME Journal 14, 999–1014 (2020).

    CAS 

    Google Scholar 

  • Jaffe, A. L. et al. Long-term incubation of lake water enables genomic sampling of consortia involving planctomycetes and candidate phyla radiation bacteria. mSystems 7, e00223–22 (2022).

    Google Scholar 

  • Cabral, L. et al. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nature Communications 13, 629 (2022).

    ADS 
    CAS 

    Google Scholar 

  • Blyton, M. D. J., Soo, R. M., Hugenholtz, P. & Moore, B. D. Characterization of the juvenile koala gut microbiome across wild populations. Environmental Microbiology 24, 4209–4219 (2022).

    CAS 

    Google Scholar 

  • Xu, B. et al. A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary. Scientific Data 9, 49 (2022).

    MathSciNet 
    CAS 

    Google Scholar 

  • Royo-Llonch, M. et al. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nature Microbiology 6, 1561–1574 (2021).

    CAS 

    Google Scholar 

  • Sun, J., Prabhu, A., Aroney, S. T. N. & Rinke, C. Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials. Microbial Genomics 8, 000842 (2022).

    CAS 

    Google Scholar 

  • Kim, M. et al. Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling. ISME Communications 2, 74 (2022).

    ADS 

    Google Scholar 

  • Kelly, J. B., Carlson, D. E., Low, J. S. & Thacker, R. W. Novel trends of genome evolution in highly complex tropical sponge microbiomes. Microbiome 10, 164 (2022).

    CAS 

    Google Scholar 

  • Bray, M. S. et al. Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes. Environmental Microbiology Reports 12, 49–57 (2020).

    CAS 

    Google Scholar 

  • Cabello-Yeves, P. J. et al. α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats. The ISME Journal 16, 2421–2432 (2022).

    CAS 

    Google Scholar 

  • Berben, T. et al. The Polar Fox Lagoon in Siberia harbours a community of Bathyarchaeota possessing the potential for peptide fermentation and acetogenesis. Antonie van Leeuwenhoek 115, 1229–1244 (2022).

    CAS 

    Google Scholar 

  • Tamburini, F. B. et al. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nature Communications 13, 926 (2022).

    ADS 
    CAS 

    Google Scholar 

  • Kantor, R. S., Miller, S. E. & Nelson, K. L. The water microbiome through a pilot scale advanced treatment facility for direct potable reuse. Frontiers in Microbiology 10, 993 (2019).

    Google Scholar 

  • Muratore, D. et al. Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nature Ecology & Evolution 6, 218–229 (2022).

    Google Scholar 

  • Zhou, Y. L., Mara, P., Cui, G. J., Edgcomb, V. P. & Wang, Y. Microbiomes in the challenger deep slope and bottom-axis sediments. Nature Communications 13, 1515 (2022).

    ADS 
    CAS 

    Google Scholar 

  • Zhang, H. et al. Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea. Scientific Data 9, 480 (2022).

    CAS 

    Google Scholar 

  • Zhuang, J. L., Zhou, Y. Y., Liu, Y. D. & Li, W. Flocs are the main source of nitrous oxide in a high-rate anammox granular sludge reactor: insights from metagenomics and fed-batch experiments. Water Research 186, e116321 (2020).

    Google Scholar 

  • Shiffman, M. E. et al. Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for eucalyptus digestion. PeerJ 5, 4075 (2017).

    Google Scholar 

  • Murphy, S. M. C., Bautista, M. A., Cramm, M. A. & Hubert, C. R. J. Diesel and crude oil biodegradation by cold-adapted microbial communities in the Labrador Sea. Applied and Environmental Microbiology 87, e00800–21 (2021).

    ADS 
    CAS 

    Google Scholar 

  • Suarez, C. et al. Metagenomic evidence of a novel family of anammox bacteria in a subsea environment. Environmental Microbiology 24, 2348–2360 (2022).

    CAS 

    Google Scholar 

  • Dharamshi, J.E. et al. Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae. The ISME Journal (2022).

  • Florian, P. O., Hugo, R. & Mathieu, A. Recovery of metagenome-assembled genomes from a human fecal sample with pacific biosciences high-fidelity sequencing. Microbiology Resource Announcements 11, e00250–22 (2022).

    Google Scholar 

  • Bloom, S. M. et al. Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation. Nature Microbiology 7, 434–450 (2022).

    CAS 

    Google Scholar 

  • Aylward, F. O. et al. Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone. Proceedings of the National Academy of Sciences 114, 11446–11451 (2017).

    ADS 
    CAS 

    Google Scholar 

  • 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 Research 25, 1043–1055 (2015).

    CAS 

    Google Scholar 

  • Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature biotechnology 35, 725 (2017).

    CAS 

    Google Scholar 

  • Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2020).

    CAS 

    Google Scholar 

  • Louca, S. The rates of global bacterial and archaeal dispersal. ISME Journal 16, 159–167 (2021).

    ADS 

    Google Scholar 

  • Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using minhash. Genome Biology 17, 132 (2016).

    Google Scholar 

  • Müllner, D. fastcluster: Fast hierarchical, agglomerative clustering routines for R and Python. Journal of Statistical Software 53, 1–18 (2013).

    Google Scholar 

  • Kinene, T., Wainaina, J., Maina, S., Boykin, L.M. & Kliman, R.M. Methods for rooting trees, vol. 3, 489–493 (Academic Press, Oxford, 2016).

  • Louca, S. & Doebeli, M. Efficient comparative phylogenetics on large trees. Bioinformatics 34, 1053–1055 (2018).

    CAS 

    Google Scholar 

  • Rees, J. A. & Cranston, K. Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal 5, e12581 (2017).

    Google Scholar 

  • Heck, K. et al. Evaluating methods for purifying cyanobacterial cultures by qPCR and high-throughput Illumina sequencing. Journal of Microbiological Methods 129, 55–60 (2016).

    CAS 

    Google Scholar 

  • Cornet, L. et al. Consensus assessment of the contamination level of publicly available cyanobacterial genomes. PLOS ONE 13, e0200323 (2018).

    Google Scholar 

  • Alneberg, J. et al. Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Microbiome 6, 173 (2018).

    Google Scholar 

  • Eddy, S. R. Accelerated profile HMM searches. PLoS Computational Biology 7, e1002195 (2011).

    ADS 
    MathSciNet 
    CAS 

    Google Scholar 

  • Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12, 59–60 (2014).

    Google Scholar 

  • Pedregosa, F. et al. Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research 12, 2825–2830 (2011).

    MathSciNet 
    MATH 

    Google Scholar 


  • Source: Ecology - nature.com

    Familiarity, age, weaning and health status impact social proximity networks in dairy calves

    Mangrove reforestation provides greater blue carbon benefit than afforestation for mitigating global climate change