A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome

Nemergut DR, Schmidt SK, Fukami T, O’Neill SP, Bilinski TM, Stanish LF, et al. Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev. 2013;77:342–56.

Sprockett D, Fukami T, Relman DA. Role of priority effects in the early-life assembly of the gut microbiota. Nat Rev Gastroenterol Hepatol. 2018;15:197–205.

Fukami T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu Rev Ecol Evol Syst. 2015;46:1–23.

• Article
• Google Scholar

Verster AJ, Borenstein E. Competitive lottery-based assembly of selected clades in the human gut microbiome. Microbiome. 2018;6:186.

Litvak Y, Bäumler AJ. The founder hypothesis: a basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens. PLOS Pathog. 2019;15:e1007563.

Zaneveld JR, Lozupone C, Gordon JI, Knight R. Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Nucleic Acids Res. 2010;38:3869–79.

Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814–21.

Wiens JJ, Ackerly DD, Allen AP, Anacker BL, Buckley LB, Cornell HV, et al. Niche conservatism as an emerging principle in ecology and conservation biology. Ecol Lett. 2010;13:1310–24.

Pyron RA, Costa GC, Patten MA, Burbrink FT. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation. Biol Rev. 2015;90:1248–62.

Losos JB. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol Lett. 2008;11:995–1003.

Darwin C. On the origin of species. London: Murray; 1859.

• Google Scholar

Ma C, Li S-p PuZ, Tan J, Liu M, Zhou J, et al. Different effects of invader–native phylogenetic relatedness on invasion success and impact: a meta-analysis of Darwin’s naturalization hypothesis. Proc R Soc B Biol Sci. 2016;283:20160663.

• Article
• Google Scholar

Peay KG, Belisle M, Fukami T. Phylogenetic relatedness predicts priority effects in nectar yeast communities. Proc R Soc B Biol Sci. 2012;279:5066.

• Article
• Google Scholar

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, et al. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science. 2016;352:586–9.

Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, et al. The prevotella copri complex comprises four distinct clades that are underrepresented in westernised populations. Cell Host Microbe. 2019;26:666–79.

Stecher B, Chaffron S, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC, et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 2010;6:e1000711.

Brown CT, Xiong W, Olm MR, Thomas BC, Baker R, Firek B, et al. Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles. mBio. 2018;9:e00441–18.

D’Andrea R, Riolo M, Ostling AM. Generalizing clusters of similar species as a signature of coexistence under competition. PloS Comput Biol. 2019;15:e1006688.

Mayfield MM, Levine JM. Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol Lett. 2010;13:1085–93.

• Article
• Google Scholar

Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. Phylogenies and community ecology. Annu Rev Ecol Evol Syst. 2002;33:475–505.

• Article
• Google Scholar

Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med. 2016;8:343ra81.

Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71:8228–35.

Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, et al. Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ. 2017;5:e2969.

Matsen FA, Evans SN, Gilks W, Ghodsi M, Kingsford C. Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. PLoS ONE. 2013;8:e56859.

Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, et al. Moving pictures of the human microbiome. Genome Biol. 2011;12:R50.

Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA. 2011;108:4578–85.

Faith DP. Conservation evaluation and phylogenetic diversity. Biol Conserv. 1992;61:1–10.

• Article
• Google Scholar

Edgar RC. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv [Preprint]. 2016. http://www.biorxiv.org/content/early/2016/10/15/081257.

Martiny JBH, Jones SE, Lennon JT, Martiny AC. Microbiomes in light of traits: a phylogenetic perspective. Science. 2015;350:649–57.

Vázquez-Baeza Y, Callewaert C, Debelius J, Hyde E, Marotz C, Morton JT, et al. Impacts of the human gut microbiome on therapeutics. Ann Rev Pharm Toxicol. 2018;58:253–70.

Scheffer M, van Nes EH. Self-organized similarity, the evolutionary emergence of groups of similar species. Proc Natl Acad Sci USA. 2006;103:6230–5.

Webb CO. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am Nat. 2000;156:145–55.

Cavender-Bares J, Ackerly DD, Baum DA, Bazzaz FA. Phylogenetic overdispersion in Floridian oak communities. Am Nat. 2004;163:823–43.

Gerhold P, Cahill JF, Winter M, Bartish IV, Prinzing A. Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better). Funct Ecol. 2015;29:600–14.

• Article
• Google Scholar

Hubbell SP. The unified neutral theory of biodiversity and biogeography. Princeton, New Jersey: Princeton University Press; 2001.

Emerson BC, Gillespie RG. Phylogenetic analysis of community assembly and structure over space and time. Trends Ecol Evol. 2008;23:619–30.

Peterfreund GL, Vandivier LE, Sinha R, Marozsan AJ, Olson WC, Zhu J, et al. Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile. PloS ONE. 2012;7:e46966.

David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 2014;15:R89.

Kennedy RC, Fling RR, Robeson MS, Saxton AM, Donnell RL, Darcy JL, et al. Temporal development of gut microbiota in triclocarban exposed pregnant and neonatal rats. Sci Rep. 2016;6:33430.

Williamson BD, Hughes JP, Willis AD. A multi-view model for relative and absolute microbial abundances. bioRxiv [Preprint]. 2019. https://www.biorxiv.org/content/early/2019/09/08/761486.

Chatzidaki-Livanis M, Geva-Zatorsky N, Comstock LE. Bacteroides fragilis type vi secretion systems use novel effector and immunity proteins to antagonize human gut bacteroidales species. Proc Natl Acad Sci USA. 2016;113:3627–32.

Hecht AL, Casterline BW, Earley ZM, Goo YA, Goodlett DR, Bubeck Wardenburg J. Strain competition restricts colonization of an enteric pathogen and prevents colitis. EMBO Rep. 2016;17:1281–91.

Sakavara A, Tsirtsis G, Roelke DL, Mancy R, Spatharis S. Lumpy species coexistence arises robustly in fluctuating resource environments. Proc Natl Acad Sci USA. 2018;115:738–43.

Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, et al. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci USA. 2011;108:1128–33.