Factors that shape the host microbiome

doi:10.1017/9781108654418.004

Chapter Four - Factors that shape the host microbiome

Published online by Cambridge University Press: 07 March 2020

Marc Sze ,

Reid N. Harris and

Edited by

Xavier A. Harrison and

Michael J. Cox

Show author details

Rachael E. Antwis: Affiliation:
University of Salford
Xavier A. Harrison: Affiliation:
University of Exeter
Michael J. Cox: Affiliation:
University of Birmingham

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Summary

Host-associated microbiomes are ubiquitous in nature, but highly variable in both space and time, and shaped by a diverse range of biotic and abiotic factors. This chapter summarises the numerous drivers of variation in microbiome structure and function across both plants and animals. Plants harbour distinct microbial communities in their rhizosphere, phyllosphere and endosphere. These communities interact with hosts in a different way, and in turn are shaped by a unique set of environmental factors. For example, the rhizosphere supports a particularly diverse microbial community shaped by plant exudates and signalling molecules to facilitate nutrient transfer to the host. Similarly, variation in animal microbiomes is driven by host genetic, life-history and environmental traits, including phylogeny, diet, age, metabolism and sociality. Several of these factors are also given more detailed treatment in later chapters. Particular attention is given to our current state of knowledge concerning initial colonisation and subsequent succession in microbial community composition in juveniles, the consequences of which remain one of the major outstanding questions in microbiome research.

Keywords

captivity colonisation development diet exudates environmental conditions host genetics metabolism ontogeny signalling molecules

Type: Chapter
Information: Microbiomes of Soils, Plants and Animals
An Integrated Approach
, pp. 55 - 77

DOI: https://doi.org/10.1017/9781108654418.004 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2020

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References

Aagaard, K, Ma, J, Antony, KM, et al. (2014) The placenta harbors a unique microbiome. Science Translational Medicine, 6, 237ra65.Google Scholar

Amato, KR. (2013) Co-evolution in context: The importance of studying the gut microbiome of wild animals. Microbiome Science, 1, 10–29.Google Scholar

Amato, KR, Yeoman, CJ, Kent, A, et al. (2013) Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME Journal, 7, 1344–1353.Google Scholar

Antwis, RE, Griffiths, SM, Harrison, XA, et al. (2017) 50 important research questions in microbial ecology. FEMS Microbiology Ecology, 93,fix044.Google Scholar

Antwis, RE, Lea, JM, Unwin, B, et al. (2018) Gut microbiome composition is associated with spatial structuring and social interactions in semi-feral Welsh Mountain ponies. Microbiome, 6, 207.Google Scholar

Archie, EA, Tung, J. (2015) Social behavior and the microbiome. Current Opinion in Behavioral Sciences, 6, 28–34.Google Scholar

Asaf, S, Khan, MA, Khan, AL, et al. (2017) Bacterial endophytes from arid land plants regulate endogenous hormone content and promote growth in crop plants: An example of Sphingomonas sp. and Serratia marcescens. Journal of Plant Interactions, 12, 31–38.Google Scholar

Augustin, R, Schröder, K, Rincón, AP, et al. (2017) A secreted antibacterial neuropeptide shapes the microbiome of Hydra. Nature Communications, 8, 698.Google Scholar

Bahrndorff, S, Bahrndorff, S, Alemu, T, et al. (2016) The microbiome of animals: Implications for conservation biology. International Journal of Genomics, 2016, 5304028.Google Scholar

Banas, JA, Loesche, WJ, Nace, GW. (1988) Possible mechanisms responsible for the reduced intestinal flora in hibernating leopard frogs (Rana pipiens). Applied and Environmental Microbiology, 54, 2311–2317.Google Scholar

Banks, JC, Craig, S, Cary, I, et al. (2009) The phylogeography of Adelie penguin faecal flora. Environmental Microbiology, 11, 577–588.Google Scholar

Banning, JL, Weddle, AL, Wahl, GW, et al. (2008) Antifungal skin bacteria, embryonic survival, and communal nesting in four-toed salamanders, Hemidactylium scutatum. Oecologia, 156, 423–429.Google Scholar

Barnes, EM, Burton, GC. (1970). The effect of hibernation on the caecal flora of the thirteen-lined ground squirrel (Citellus tridecemlineatus). Journal of Applied Bacteriology, 33, 505–514.Google Scholar

Bataille, A, Lee-Cruz, L, Tripathi, B, et al. (2016) Microbiome variation across amphibian skin regions: Implications for chytridiomycosis mitigation efforts. Microbial Ecology, 71, 221–232.Google Scholar

Bates, KA, Clare, FC, O’Hanlon, S, et al. (2018) Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure. Nature Communications, 9, 693.Google Scholar

Becker, MH, Richards-Zawacki, CL, Gratwicke, B, et al. (2014) The effect of captivity on the cutaneous bacterial community of the critically endangered Panamanian golden frog (Atelopus zeteki). Biological Conservation, 176, 199–206.Google Scholar

Bennett, KD. (1997) Evolution and Ecology: The Pace of Life. Cambridge: Cambridge University Press.Google Scholar

Berendsen, RL, Pieterse, CM, Bakker, PA. (2012) The rhizosphere microbiome and plant health. Trends in Plant Science, 17, 478–486.Google Scholar

Billiet, A, Meeus, I, Van Nieuwerburgh, F, et al. (2017) Colony contact contributes to the diversity of gut bacteria in bumblebees (Bombus terrestris). Insect Science, 24, 270–277.Google Scholar

Bollaerts, K, Riera-Montes, M, Heininger, U, et al. (2017) A systematic review of varicella seroprevalence in European countries before universal childhood immunization: Deriving incidence from seroprevalence data. Epidemiology & Infection, 145, 2666–2677.Google Scholar

Bolnick, DI, Snowberg, LK, Caporaso, JG, et al. (2014) Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Molecular Ecology, 23, 4831–4845.Google Scholar

Borruso, L, Bacci, G, Mengoni, A, et al. (2014) Rhizosphere effect and salinity competing to shape microbial communities in Phragmites australis (Cav.) Trin. ex-Steud. FEMS Microbiology Letters, 359, 193–200.Google Scholar

Bosch, TCG, McFall-Ngai, MJ. (2011) Metaorganisms as the new frontier. Zoology, 114, 185–190.Google Scholar

Broderick, NA, Lemaitre, B. (2012) Gut-associated microbes of Drosophila melanogaster. Gut Microbes, 3, 307–321.Google Scholar

Brucker, RM, Bordenstein, SR. (2013) The hologenomic basis of speciation: Gut bacteria cause hybrid lethality in the genus Nasonia. Science, 341, 667–669.Google Scholar

Bula-Rudas, FJ, Rathore, MH, Maraqa, NF. (2015) Salmonella infections in childhood. Advances in Pediatrics, 62, 29–58.Google Scholar

Burch, AY, Zeisler, V, Yokota, K, et al. (2014) The hygroscopic biosurfactant syringafactin produced by Pseudomonas syringae enhances fitness on leaf surfaces during fluctuating humidity. Environmental Microbiology, 16, 2086–2098.Google Scholar

Burch, AY, Do, PT, Sbodio, A, et al. (2016) High-level culturability of epiphytic bacteria and frequency of biosurfactant producers on leaves. Applied and Environmental Microbiology, 82, 5997.Google Scholar

Campbell, LJ, Garner, TW, Hopkins, K, et al. (2019) Outbreaks of an emerging viral disease covary with differences in the composition of the skin microbiome of a wild UK amphibian. Frontiers in Microbiology, 10, 1245.Google Scholar

Cherel, Y, Charrassin, JB, Challet, E. (1994) Energy and protein requirements for molt in the king penguin Aptenodytes patagonicus. American Journal of Physiology: Regulatory, Integrative and Comparative Physiology, 266, R1182–1188.Google Scholar

Clayton, JB, Vangay, P, Huang, H, et al. (2016) Captivity humanizes the primate microbiome. Proceedings of the National Academy of Sciences, 113, 10376–10381.Google Scholar

Coleman‐Derr, D, Desgarennes, D, Fonseca‐Garcia, C, et al. (2016) Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytologist, 209, 798–811.Google Scholar

Colston, TJ. (2017) Gut microbiome transmission in lizards. Molecular Ecology, 26, 972–974.Google Scholar

Cooper, RG. (2004) Ostrich (Struthio camelus) chick and grower nutrition. Animal Science Journal, 75, 487–490.Google Scholar

Cordier, T, Robin, C, Capdevielle, X, et al. (2012) The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica) varies significantly along an elevation gradient. New Phytologist, 196, 510–519.Google Scholar

Costello, EK, Gordon, JI, Secor, SM, et al. (2010) Postprandial remodeling of the gut microbiota in Burmese pythons. The ISME Journal, 4, 1375–1385.Google Scholar

Davenport, ER, Sanders, JG, Song, SJ, et al. (2017) The human microbiome in evolution. BMC Biology, 15, 1–12.Google Scholar

David, LA, Maurice, CF, Carmody, RN, et al. (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505, 559.Google Scholar

Degnan, PH, Pusey, AE, Lonsdorf, EV, et al. (2012) Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park. Proceedings of the National Academy of Sciences, 109, 13034–13039.Google Scholar

Delport, TC, Power, ML, Harcourt, RG, et al. (2016) Colony location and captivity influence the gut microbial community composition of the Australian sea lion (Neophoca cinerea). Applied and Environmental Microbiology, 82, 3440–3449.Google Scholar

Delsuc, F, Metcalf, JL, Wegener Parfrey, L, et al. (2014) Convergence of gut microbiomes in myrmecophagous mammals. Molecular Ecology, 23, 1301–1317.CrossRef Google Scholar PubMed

Dewar, ML, Arnould, JP, Krause, L, et al. (2014) Influence of fasting during moult on the faecal microbiota of penguins. PLoS ONE, 9, e99996.Google Scholar

Dominguez-Bello, MG, Costello, EK, Contreras, M, et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107, 11971–11975.Google Scholar

Dominguez-Bello, MG, De Jesus-Laboy, KM, Shen, N, et al. (2016) Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine, 22, 250.Google Scholar

Douglas, AE. (2015) Multiorganismal insects: Diversity and function of resident microorganisms. Annual Review of Entomology, 60, 17–34.Google Scholar

Duca, FA, Sakar, Y, Lepage, P, et al. (2014) Replication of obesity and associated signaling pathways through transfer of microbiota from obese-prone rats. Diabetes, 63, 1624–36.Google Scholar

Duca, FA, Sakar, Y, Lepage, P, et al. (2016) Statement of retraction. Replication of obesity and associated signaling pathways through transfer of microbiota from obese-prone rats. Diabetes, 63, 1624–1636.Google Scholar

Duncan, SH, Belenguer, A, Holtrop, G, et al. (2007) Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Applied and Environmental Microbiology, 73, 1073–1078.Google Scholar

Eaves, LJ, Last, KA, Young, PA, Martin, NG. (1978) Model-fitting approaches to the analysis of human behaviour. Heredity, 41, 249–320.Google Scholar

Egamberdieva, D, Jabborova, D, Berg, G. (2016) Synergistic interactions between Bradyrhizobium japonicum and the endophyte Stenotrophomonas rhizophila and their effects on growth, and nodulation of soybean under salt stress. Plant and Soil, 405, 35–45.Google Scholar

Ellner, PD. (1998) Smallpox: Gone but not forgotten. Infection, 26, 263–269.Google Scholar

Feng, Q, Chen, WD, Wang, YD. (2018) Gut microbiota: An integral moderator in health and disease. Frontiers in Microbiology, 9, 151.Google Scholar

Finucane, MM, Sharpton, TJ, Laurent, TJ, et al. (2014) A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS ONE, 9, e84689.Google Scholar

Fitzpatrick, BM, Allison, AL. (2014) Similarity and differentiation between bacteria associated with skin of salamanders (Plethodon jordani) and free-living assemblages. FEMS Microbiology Ecology, 88, 482–94.Google Scholar

Flint, HJ, Bayer, EA, Rincon, MT, et al. (2008) Polysaccharide utilization by gut bacteria: Potential for new insights from genomic analysis. Nature Reviews Microbiology, 6, 121–131.Google Scholar

Fraust, K, Raes, J. (2012) Microbial interactions: From networks to models. Nature Reviews Microbiology, 10, 538–550.Google Scholar

Froussart, E, Bonneau, J, Franche, C, et al. (2016) Recent advances in actinorhizal symbiosis signaling. Plant Molecular Biology, 90, 613–22.Google Scholar

Funkhouser, LJ, Bordenstein, SR. (2013) Mom knows best: The universality of maternal microbial transmission. PLoS Biology, 11, e1001631.Google Scholar

Gabutti, G, Franchi, M, Maniscalco, L, et al. (2016) Varicella-zoster virus: Pathogenesis, incidence patterns and vaccination programs. Minerva Pediatrica, 68, 213–225.Google Scholar

Gause, G. (1934) The Struggle for Existence. New York, NY: Dover Publications.Google Scholar

Gauthier-Clerc, M, Le Maho, Y, Clerquin, Y, et al. (2002) Seabird reproduction in an unpredictable environment: How king penguins provide their young chicks with food. Marine Ecology Progress Series, 237, 291–300.Google Scholar

Geller, LT, Barzily-Rokni, M, Danino, T, et al. (2017) Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science, 357, 1156–1160.Google Scholar

Gevers, D, Knight, R, Petrosino, JF, et al. (2012) The Human Microbiome Project: A community resource for the healthy human microbiome. PLoS Biology, 10, e1001377.Google Scholar

Godoy-Vitorino, F, Goldfarb, KC, Brodie, EL, et al. (2010) Developmental microbial ecology of the crop of the folivorous hoatzin. The ISME Journal, 4, 611.Google Scholar

Goodrich, JK, Waters, JL, Poole, AC, et al. (2014) Human genetics shape the gut microbiome. Cell, 159, 789–99.Google Scholar

Gossling, J, Loesche, WJ, Nace, GW. (1982a) Large intestine bacterial flora of nonhibernating and hibernating leopard frogs (Rana pipiens). Applied and Environmental Microbiology, 44, 59–66.Google Scholar

Gossling, J, Loesche, WJ, Nace, GW. (1982b) Response of intestinal flora of laboratory-reared leopard frogs (Rana pipiens) to cold and fasting. Applied and Environmental Microbiology, 44, 67–71.Google Scholar

Gottel, NR, Castro, HF, Kerley, M, et al. (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Applied and Environmental Microbiology, 77, 5934–5944.Google Scholar

Grieneisen, LE, Livermore, J, Alberts, S, et al. (2017) Group living and male dispersal predict the core gut microbiome in wild baboons. Integrative and Comparative Biology, 57, 770–785.Google Scholar

Griffiths, SM, Harrison, XA, Weldon, C, et al. (2018) Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian. The ISME Journal, 12, 2506.Google Scholar

Griffiths, SM, Antwis, RE, Lenzi, L, et al. (2019) Host genetics and geography influence microbiome composition in the sponge Ircinia campana. Journal of Animal Ecology, DOI:10.1111/1365-2656.13065.Google Scholar

Groscolas, R, Robin, JP. (2001) Long-term fasting and re-feeding in penguins. Comparative Biochemistry and Physiology Part A: Molecular and Integrative Physiology, 128, 645–655.Google Scholar

Gómez-Brandón, M, Lores, M, Domínguez, J. (2012) Species-specific effects of epigeic earthworms on microbial community structure during first stages of decomposition of organic matter. PLoS ONE, 7, e31895.Google Scholar

Hallmann, J, Quadt-Hallmann, A, Mahaffee, WF, et al. (1997) Bacterial endophytes in agricultural crops. Canadian Journal of Microbiology, 43, 895–914.Google Scholar

Hammer, TJ, Bowers, MD. (2015) Gut microbes may facilitate insect herbivory of chemically defended plants. Oecologia, 179, 1–14.Google Scholar

Hehemann, JH, Kelly, AG, Pudlo, NA, et al. (2012) Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proceedings of the National Academy of Sciences, 109, 19786–19791.Google Scholar

Hird, SM. (2017) Evolutionary biology needs wild microbiomes. Frontiers in Microbiology, 8, 725.Google Scholar

House, D, Bishop, A, Parry, C, et al. (2001) Typhoid fever: Pathogenesis and disease. Current Opinion in Infectious Diseases, 14, 573–578.Google Scholar

Hufeldt, MR, Nielsen, DS, Vogensen, FK, et al. (2010) Variation in the gut microbiota of laboratory mice is related to both genetic and environmental factors. Comparative Medicine, 60, 336–347.Google Scholar

Human Microbiome Consortium. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207–214.Google Scholar

Iniguez, AL, Dong, Y, Carter, HD, et al. (2005) Regulation of enteric endophytic bacterial colonization by plant defenses. Molecular Plant–Microbe Interactions, 18, 169–178.Google Scholar

Kandel, S, Joubert, P, Doty, S. (2017) Bacterial endophyte colonization and distribution within plants. Microorganisms, 5, 77.Google Scholar

Keenan, SW, Engel, AS, Elsey, RM. (2013) The alligator gut microbiome and implications for archosaur symbioses. Scientific Reports, 3, 2877.Google Scholar

Kohl, KD, Cary, TL, Karasov, WH, et al. (2013) Restructuring of the amphibian gut microbiota through metamorphosis. Environmental Microbiology Reports, 5, 899–903.Google Scholar

Kohl, KD, Brun, A, Magallanes, M, et al. (2017) Gut microbial ecology of lizards: Insights into diversity in the wild, effects of captivity, variation across gut regions and transmission. Molecular Ecology, 26, 1175–1189.Google Scholar

Kong, F, Zhao, J, Han, S, et al. (2014) Characterization of the gut microbiota in the red panda (Ailurus fulgens). PLoS ONE, 9, e87885.Google Scholar

Kreisinger, J, Čížková, D, Vohánka, J, et al. (2014) Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high‐throughput parallel pyrosequencing. Molecular Ecology, 23, 5048–5060.Google Scholar

Kueneman, JG, Parfrey, LW, Woodhams, DC, et al. (2014) The amphibian skin‐associated microbiome across species, space and life history stages. Molecular Ecology, 23, 1238–1250.Google Scholar

Kueneman, JG, Woodhams, DC, Harris, R, et al. (2016) Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity. Proceedings of the Royal Society B: Biological Sciences, 283, 20161553.Google Scholar

Kulkarni, S, Heeb, P. (2007) Social and sexual behaviours aid transmission of bacteria in birds. Behavioral Processes, 74, 88–92.Google Scholar

Kwong, WK, Moran, NA. (2015) Evolution of host specialization in gut microbes: The bee gut as a model. Gut Microbes, 6, 214–220.Google Scholar

Larrainzar, E, Wienkoop, S. (2017) A proteomic view on the role of legume symbiotic interactions. Frontiers in Plant Science, 8, 1267.Google Scholar

Lax, S, Smith, DP, Hampton-Marcell, J, et al. (2014) Longitudinal analysis of microbial interaction between humans and the indoor environment. Science, 345, 1048–1052.Google Scholar

Ley, RE, Bäckhed, F, Turnbaugh, P, et al. (2005) Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences, 102, 11070–11075.Google Scholar

Ley, RE, Turnbaugh, PJ, Klein, S, et al. (2006) Microbial ecology: Human gut microbes associated with obesity. Nature, 444, 1022.Google Scholar

Ley, RE, Hamady, M, Lozupone, C, et al. (2008a) Evolution of mammals and their gut microbes. Science, 320, 1647–1651.Google Scholar

Ley, RE, Lozupone, CA, Hamady, M, et al. (2008b) Worlds within worlds: Evolution of the vertebrate gut microbiota. Nature Reviews Microbiology, 6, 776.Google Scholar

Li, Z, Wright, AD, Si, H, et al. (2016) Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses. Environmental Microbiology Reports, 8, 1016–1023.Google Scholar

Loudon, AH, Woodhams, DC, Parfrey, LW, et al. (2014) Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus). The ISME Journal, 8, 830.Google Scholar

Lu, J, Idris, U, Harmon, B, et al. (2003) Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Applied and Environmental Microbiology, 69, 6816–6824.Google Scholar

Macke, E, Tasiemski, A, Massol, F, et al. (2017) Life history and eco‐evolutionary dynamics in light of the gut microbiota. Oikos, 126, 508–531.Google Scholar

Mamantopoulos, M, Ronchi, F, Van Hauwermeiren, F, et al. (2017) Nlrp6-and ASC-dependent inflammasomes do not shape the commensal gut microbiota composition. Immunity, 47, 339–348.Google Scholar

Martin, FM, Uroz, S, Barker, DG. (2017) Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria. Science, 356, eaad4501.Google Scholar

Mazel, F, Davis, KM, Loudon, A, et al. (2018) Is host filtering the main driver of phylosymbiosis across the tree of life? mSystems, 3, e00097–18.Google Scholar

McFall-Ngai, M, Hadfield, MG, Bosch, TC, et al. (2013) Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110, 3229–3236.Google Scholar

McKenzie, VJ, Song, SJ, Delsuc, F, et al. (2017) The effects of captivity on the mammalian gut microbiome. Integrative and Comparative Biology, 57, 690–704.Google Scholar

Melotto, M, Underwood, W, Koczan, J, et al. (2006) Plant stomata function in innate immunity against bacterial invasion. Cell, 126, 969–980.Google Scholar

Melotto, M, Zhang, L, Oblessuc, PR, et al. (2017) Stomatal defense a decade later. Plant Physiology, 174, 561–571.Google Scholar

Mendes, R, Kruijt, M, De Bruijn, I, et al. (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science, 332, 1097–1100.Google Scholar

Menke, S, Melzheimer, J, Thalwitzer, S, et al. (2017) Gut microbiomes of free‐ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens. Molecular Ecology, 26, 5515–5527.Google Scholar

Muegge, BD, Kuczynski, J, Knights, D, et al. (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science, 332, 970–974.Google Scholar

Nelson, TM, Rogers, TL, Carlini, AR, et al. (2013) Diet and phylogeny shape the gut microbiota of Antarctic seals: A comparison of wild and captive animals. Environmental Microbiology, 15, 1132–1145.Google Scholar

Noyer, C, Becerro, MA. (2012) Relationship between genetic, chemical, and bacterial diversity in the Atlanto-Mediterranean bath sponge Spongia lamella. Hydrobiologia, 687, 85–99.Google Scholar

Oldroyd, GE, Murray, JD, Poole, PS, et al. (2011) The rules of engagement in the legume–rhizobial symbiosis. Annual Review of Genetics, 45, 119–144.Google Scholar

Oliver, KM, Degnan, PH, Burke, GR, et al. (2010) Facultative symbionts in aphids and the horizontal transfer of ecologically important traits. Annual Review of Entomology, 55, 247–266.Google Scholar

Panchal, S, Roy, D, Chitrakar, R, et al. (2016) Coronatine facilitates Pseudomonas syringae infection of Arabidopsis leaves at night. Frontiers in Plant Science, 7, 880.Google Scholar

Parvaiz, A, Satyawati, S. (2008) Salt stress and phyto-biochemical responses of plants – A review. Plant Soil Environment, 54, 89–99.Google Scholar

Pascoe, EL, Hauffe, HC, Marchesi, JR, Perkins, SE. (2017) Network analysis of gut microbiota literature: An overview of the research landscape in non-human animal studies. The ISME Journal, 11, 2644.Google Scholar

Philippot, L, Raaijmakers, JM, Lemanceau, P, et al. (2013) Going back to the roots: The microbial ecology of the rhizosphere. Nature Reviews Microbiology, 11, 789.Google Scholar

Pieterse, CM, Zamioudis, C, Berendsen, RL, et al. (2014) Induced systemic resistance by beneficial microbes. Annual Review of Phytopathology, 52, 347–375.Google Scholar

Pietschke, C, Treitz, C, Forêt, S, et al. (2017) Host modification of a bacterial quorum-sensing signal induces a phenotypic switch in bacterial symbionts. Proceedings of the National Academy of Sciences, 114, E8488–8497.Google Scholar

Redford, KH, Segre, JA, Salafsky, N, et al. (2012) Conservation and the microbiome. Conservation Biology, 2012, 195–197.Google Scholar

Ren, G, Zhang, H, Lin, X, et al. (2015) Response of leaf endophytic bacterial community to elevated CO₂ at different growth stages of rice plant. Frontiers in Microbiology, 6, 855.Google Scholar

Rosenblueth, M, Martínez-Romero, E. (2006) Bacterial endophytes and their interactions with hosts. Molecular Plant–Microbe Interactions, 19, 827–837.Google Scholar

Rosshart, SP, Vassallo, BG, Angeletti, D, et al. (2017) Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell, 171, 1015–1028.Google Scholar

Santoyo, G, Moreno-Hagelsieb, G, del Carmen Orozco-Mosqueda, M, et al. (2016) Plant growth-promoting bacterial endophytes. Microbiological Research, 183, 92–99.Google Scholar

Sasse, J, Martinoia, E, Northen, T. (2018) Feed your friends: Do plant exudates shape the root microbiome? Trends in Plant Science, 23, 25–41.Google Scholar

Schubert, AM, Sinani, H, Schloss, PD. (2015) Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile. mBio, 6, e00974–15.Google Scholar

Seedorf, H, Griffin, NW, Ridaura, VK, et al. (2014) Bacteria from diverse habitats colonize and compete in the mouse gut. Cell, 159, 253–266.Google Scholar

Sender, R, Fuchs, S, Milo, R. (2016a) Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164, 337–340.Google Scholar

Sender, R, Fuchs, S, Milo, R. (2016b) Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14, e1002533.Google Scholar

Shah, MS, DeSantis, TZ, Weinmaier, T, et al. (2018) Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer. Gut, 67, 882–891.Google Scholar

Smith, CC, Snowberg, LK, Caporaso, JG, et al. (2015) Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota. The ISME Journal, 9, 2515.Google Scholar

Song, SJ, Lauber, C, Costello, EK, et al. (2013) Cohabiting family members share microbiota with one another and with their dogs. eLife, 2, e00458.Google Scholar

Sonoyama, K, Fujiwara, R, Takemura, N, et al. (2009) Response of gut microbiota to fasting and hibernation in Syrian hamsters. Journal of Applied Environmental Microbiology, 75, 6451–6456.Google Scholar

Sze, MA, Schloss, PD. (2016) Looking for a signal in the noise: Revisiting obesity and the microbiome. mBio, 7, e01018–16.Google Scholar

Sze, MA, Schloss, PD. (2018) Leveraging existing 16S rRNA gene surveys to identify reproducible biomarkers in individuals with colorectal tumors. mBio, 9, e00630–18.Google Scholar

Sze, MA, Tsuruta, M, Yang, SW, et al. (2014) Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs. PLoS ONE, 9, e111228.Google Scholar

Thakuria, D, Schmidt, O, Finan, D, et al. (2010) Gut wall bacteria of earthworms: A natural selection process. The ISME Journal, 4, 357.Google Scholar

Thomas, T, Moitinho-Silva, L, Lurgi, M, et al. (2016) Diversity, structure and convergent evolution of the global sponge microbiome. Nature Communications, 7, 11870.Google Scholar

Thompson, LR, Sanders, JG, McDonald, D, et al. (2017) A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551, 457.Google Scholar

Trevelline, BK, Fontaine, SS, Hartup, BK, et al. (2019) Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proceedings of the Royal Society B: Biological Sciences, 286, 20182448.Google Scholar

Tung, J, Barreiro, LB, Burns, MB, et al. (2015) Social networks predict gut microbiome composition in wild baboons. eLife, 4, e05224.Google Scholar

Turnbaugh, PJ, Ley, RE, Mahowald, MA, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444, 1027.Google Scholar

Turnbaugh, PJ, Hamady, M, Yatsunenko, T, et al. (2009a) A core gut microbiome in obese and lean twins. Nature, 457, 480.Google Scholar

Turnbaugh, PJ, Ridaura, VK, Faith, JJ, et al. (2009b) The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Science Translational Medicine, 1, 6ra14.Google Scholar

Turner, TR, James, EK, Poole, PS. (2013) The plant microbiome. Genome Biology, 14, 209.Google Scholar

Tveit, AT, Urich, T, Frenzel, P, et al. (2015) Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proceedings of the National Academy of Sciences, 112, E2507–2516.Google Scholar

Vacher, C, Hampe, A, Porté, AJ, et al. (2016) The phyllosphere: Microbial jungle at the plant–climate interface. Annual Review of Ecology, Evolution, and Systematics, 47, 1–24.Google Scholar

Videvall, E, Song, SJ, Bensch, HM, et al. (2019) Major shifts in gut microbiota during development and its relationship to growth in ostriches. Molecular Ecology, 28, 2653–2667.Google Scholar

Von Mutius, E. (2016) The microbial environment and its influence on asthma prevention in early life. The Journal of Allergy and Clinical Immunology, 137, 680–689.Google Scholar

Waite, DW, Eason, D, Taylor, MW. (2014) Influence of hand rearing and bird age on the fecal microbiota of the critically endangered kakapo. Applied and Environmental Microbiology, 80, 4650–4658.Google Scholar

Walke, JB, Harris, RN, Reinert, LK, et al. (2011) Social immunity in amphibians: Evidence for vertical transmission of innate defenses. Biotropica, 43, 396–400.Google Scholar

Walke, JB, Becker, MH, Loftus, SC, et al. (2014) Amphibian skin may select for rare environmental microbes. The ISME Journal, 8, 2207.Google Scholar

Walters, WA, Xu, Z, Knight, R. (2014) Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Letters, 588, 4223–4233.Google Scholar

Wang, W, Zheng, S, Sharshov, K, et al. (2016) Distinctive gut microbial community structure in both the wild and farmed swan goose (Anser cygnoides). Journal of Basic Microbiology, 56, 1299–1307.Google Scholar

Wasimuddin, , Menke, S, Melzheimer, J, et al. (2017) Gut microbiomes of free-ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens. Molecular Ecology, 26.Google Scholar

Weinert, N, Piceno, Y, Ding, GC, et al. (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: Many common and few cultivar-dependent taxa. FEMS Microbiology Ecology, 75, 497–506.Google Scholar

White, J, Mirleau, P, Danchin, E, et al. (2010) Sexually transmitted bacteria affect female cloacal assemblages in a wild bird. Ecology Letters, 13, 1515–1524.Google Scholar

White, J, Richard, M, Massot, M, Meylan, S. (2011) Cloacal bacterial diversity increases with multiple mates: Evidence of sexual transmission in female common lizards. PLoS ONE, 6, e22339.Google Scholar

Wienemann, T, Schmitt-Wagner, D, Meuser, K, et al. (2011) The bacterial microbiota in the ceca of Capercaillie (Tetrao urogallus) differs between wild and captive birds. Systematic and Applied Microbiology, 34, 542–551.Google Scholar

Williams, CL, Willard, S, Kouba, A, et al. (2013) Dietary shifts affect the gastrointestinal microflora of the giant panda (Ailuropoda melanoleuca). Journal of Animal Physiology and Animal Nutrition, 97, 577–585.Google Scholar

Wong, S, Stephens, WZ, Burns, AR, et al. (2015) Ontogenetic differences in dietary fat influence microbiota assembly in the zebrafish gut. mBio, 6, e00687–15.Google Scholar

Wu, GD, Chen, J, Hoffmann, C, et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science, 334, 105–108.Google Scholar

Xie, Y, Xia, P, Wang, H, et al. (2016) Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis). Scientific Reports, 6, 33350.Google Scholar

Xue, Z, Zhang, W, Wang, L, et al. (2015) The bamboo-eating giant panda harbors a carnivore-like gut microbiota, with excessive seasonal variations. mBio, 6, e00022–15.Google Scholar

Yang, SC, Lin, CH, Aljuffali, IA, Fang, JY. (2017). Current pathogenic Escherichia coli foodborne outbreak cases and therapy development. Archives of Microbiology, 199, 811–825.Google Scholar

Yildirim, S, Yeoman, CJ, Janga, SC, et al. (2014) Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance. The ISME Journal, 8, 2431–2444.Google Scholar

Youngblut, ND, Reischer, GH, Walters, W, et al. (2019). Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nature Communications, 10, 2200.Google Scholar

Yuan, ML, Dean, SH, Longo, AV, et al. (2015) Kinship, inbreeding and fine‐scale spatial structure influence gut microbiota in a hindgut‐fermenting tortoise. Molecular Ecology, 24, 2521–2536.Google Scholar

Zgadzaj, R, Garrido-Oter, R, Jensen, DB, et al. (2016) Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proceedings of the National Academy of Sciences, 113, E7996.Google Scholar

Zheng, H, Powell, JE, Steele, MI, et al. (2017) Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Proceedings of the National Academy of Sciences, 114, 4775–4780.Google Scholar

Zoetendal, EG, Akkermans, ADL, Vliet, WMA, et al. (2001) The host genotype affects the bacterial community in the human gastronintestinal tract. Microbial Ecology in Health and Disease, 13, 129–134.Google Scholar

Zwirglmaier, K, Keiz, K, Engel, M, et al. (2015) Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria. Frontiers in Microbiology, 6, 1168.Google Scholar

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Chapter Four - Factors that shape the host microbiome

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