No Genome is an Island Extra References 7
7.
Symbiotic Associations, Microbiomes, and Holobionts
· 7.A. Microbiomes and their
effects.
o Human
microbiome composition and effects. (Peterson, Garges et al. 2009;
Turnbaugh and Gordon 2009; Ellrott, Jaroszewski et al. 2010;
Jakobsson, Jernberg et al. 2010; Jones, Sun et al. 2010; Arora
and Sharma 2011; Arumugam, Raes et al. 2011; Boerner and
Sarvetnick 2011; Caporaso, Lauber et al. 2011; Cryan and
O'Mahony 2011; Kinross, Darzi et al. 2011; Morowitz, Babrowski
et al. 2011; Parfrey, Walters et al. 2011; Smillie, Smith et
al. 2011; Tilg and Kaser 2011; Weinstock 2011; Consortium
2012; Gevers, Knight et al. 2012; Grice and Segre 2012; Koren,
Goodrich et al. 2012; Lagier, Armougom et al. 2012;
Romano-Keeler, Weitkamp et al. 2012; Kim, Jeon et al. 2013;
Lepage, Leclerc et al. 2013; Schwabe and Jobin 2013; Smith,
Yatsunenko et al. 2013; Vindigni, Broussard et al. 2013;
Allegretti and Hamilton 2014; Bultman 2014; Cenit, Matzaraki
et al. 2014; Doerflinger, Throop et al. 2014; Gilbert 2014;
Goodrich, Waters et al. 2014; Li, Jia et al. 2014; Ye 2014;
Zhu, Liu et al. 2014; Clemente and Erica C. Pehrsson 2015;
Dash, Clarke et al. 2015; Allen, Dinan et al. 2017; Davenport,
Sanders et al. 2017; Hasegawa, Mark Welch et al. 2017; Hoban,
Stilling et al. 2017; Kundu, Blacher et al. 2017; Tropini,
Earle et al. 2017; Gopalakrishnan, Spencer et al. 2018;
Johnson and Foster 2018; Matson, Fessler et al. 2018;
Zitvogel, Ma et al. 2018)
The composition of our microbiome affects
- metabolism
and digestion over the course of our lifetime (Turnbaugh and Gordon
2009; Tilg and Kaser 2011; Romano-Keeler, Weitkamp
et al. 2012; Kundu, Blacher et al. 2017)
- changes
during pregnancy (Koren,
Goodrich et al. 2012),
- our immune
responses (Doerflinger,
Throop et al. 2014; Salvucci 2014)
(including autoimmunity (Boerner and Sarvetnick 2011)
- cancer
immunotherapy (Zitvogel,
Ma et al. 2018))
- our states
of mind (Cryan and
O'Mahony 2011; Dash, Clarke et al. 2015; Allen,
Dinan et al. 2017; Hoban, Stilling et al. 2017).
o Each organ or area of the
human body has its own microbiome
§ Different skin regions and
mucosal surfaces
(Gill, Pop et al. 2006; Aziz 2009;
Grice, Kong et al. 2009; Hamady and Knight 2009; Peterson,
Garges et al. 2009; Ellrott, Jaroszewski et al. 2010; Jones,
Sun et al. 2010; Kuczynski, Costello et al. 2010; Grice and
Segre 2011; Moissl-Eichinger, Probst et al. 2017; Chen,
Fischbach et al. 2018)
·
Throat
(Jakobsson, Jernberg et al. 2010)
§ The gut microbiome (Gill, Pop et al. 2006; Aziz 2009;
Turnbaugh and Gordon 2009; Ellrott, Jaroszewski et al. 2010;
Kinross, Darzi et al. 2011)
·
suppresses invasion by
bacterial pathogens
(Peixoto, Alves et al. 2017)
·
Pathogen
elimination by probiotic Bacillus via
signalling interference of Staphylococcus aureus (Piewngam, Zheng et al. 2018).
§ Previously unknown
bacterial taxa discovered in gut microbiome
(Nelson, Weinstock et al. 2010;
Consortium 2012; Wylie, Truty et al. 2012).
o Human gut
microbiome coding capacity. Estimates
of the genomic coding complexity of the human gut microbiome
range from 3.3 to 9.9 million distinct proteins, or 150X - 450X
greater than the basic human proteome
(Yang, Xie et al. 2009; Zhu, Wang et
al. 2010; Donia, Cimermancic et al. 2014; Li, Jia et al. 2014).
When the diverse microbiomes existing in and on other body
locations are considered
(Grice and Segre 2012), the difference
becomes even more striking.
(Zhu, Wang et al. 2010)
o Non-human
microbiomes. (Suen, Scott et al. 2010; Shin, Kim
et al. 2011; Berg Miller, Yeoman et al. 2012; Cho, Yamanishi
et al. 2012; Hentschel, Piel et al. 2012; Looft and Allen
2012; Lundberg, Lebeis et al. 2012; Cheng, Tian et al. 2013;
Weiss, Wang et al. 2013; Passos da Silva, Castaneda-Ojeda et
al. 2014; Pinto, Pinho et al. 2014; Edwards, Johnson et al.
2015; Lebeis, Paredes et al. 2015; Panke-Buisse, Poole et
al. 2015; Sunagawa, Coelho et al. 2015; Vandenkoornhuyse,
Quaiser et al. 2015; Zarraonaindia, Owens et al. 2015;
Agler, Ruhe et al. 2016; Berg, Rybakova et al. 2016; Liu,
Carvalhais et al. 2017; Murillo-Rincon, Klimovich et al.
2017; Perez-Jaramillo, Carrion et al. 2017; Stolz 2017;
Garcia-Bonilla, Brandao et al. 2018; Ivens, Gadau et al.
2018; Moissl-Eichinger, Pausan et al. 2018; Raymann and
Moran 2018)
o Bacterial-Archaeal
Syntrophy and Conflict: (Stams and Plugge 2009; Edgcomb,
Leadbetter et al. 2011; Wrede, Dreier et al. 2012;
Atanasova, Pietila et al. 2013; Anderson, Sogin et al. 2014;
Wegener, Krukenberg et al. 2015; Koskinen, Pausan et al.
2017; Moissl-Eichinger, Probst et al. 2017; Jin, Li et al.
2018; Moissl-Eichinger, Pausan et al. 2018)
· 7.B. Holobiont evolution
o Holobiont concept. (Margulis 1991; Zrzavy and Skala
1993; Guerrero, Margulis et al. 2013; Salvucci 2014;
Bordenstein and Theis 2015; Vandenkoornhuyse, Quaiser et al.
2015; Diaz-Munoz, Boddy et al. 2016; Rosenberg and
Zilber-Rosenberg 2016; Shropshire and Bordenstein 2016; Theis,
Dheilly et al. 2016; Adair and Douglas 2017; Koskella, Hall et
al. 2017; Rees, Bosch et al. 2018; Rosenberg and
Zilber-Rosenberg 2018; Sandoval-Motta, Aldana et al. 2018)
o The term “holobiont” applied to metazoa: sponges
(Pita, Rix et al. 2018), corals holobiont
(Thompson, Rivera et al. 2014; van
de Water, Allemand et al. 2018),
tsetse flies (Snyder and Rio 2013),
and bark beetles (Six 2013).
o
Amoeba and other protists
that are phagocytic, engulf other microorganisms, and serve
as hosts to bacteria
like Legionella, Helicobacter,
Listeria, and Mycobacterium that also infect animal
cells (Gomez-Valero and Buchrieser 2013;
Yousuf, Siddiqui et al. 2013; Hoffmann, Harrison et al.
2014).
o
Protist
“Melting Pots” In other words, Acanthamoeba protists
and animal guts constitute evolutionary “melting pots,” where
new adaptations can arise and then be transferred symbiotically
to other organisms
(Boyer, Yutin et al. 2009; Moliner,
Fournier et al. 2010; Shterzer and Mizrahi 2015; Guimaraes,
Gomes et al. 2016; Wang and Wu 2017).
REFERENCES
Adair, K. L. and A. E.
Douglas (2017). "Making a microbiome: the many determinants of
host-associated microbial community composition." Curr
Opin Microbiol 35:
23-29. http://www.ncbi.nlm.nih.gov/pubmed/27907842.
Agler, M. T., J. Ruhe,
et al. (2016). "Microbial Hub Taxa Link Host and Abiotic
Factors to Plant Microbiome Variation." PLoS Biol 14(1): e1002352. http://www.ncbi.nlm.nih.gov/pubmed/26788878.
Allegretti, J. R. and M.
J. Hamilton (2014). "Restoring the gut microbiome for the
treatment of inflammatory bowel diseases." World J
Gastroenterol 20(13):
3468-3474. http://www.ncbi.nlm.nih.gov/pubmed/24707129.
Allen, A. P., T. G.
Dinan, et al. (2017). "A psychology of the human
brain-gut-microbiome axis." Soc Personal Psychol Compass
11(4): e12309. http://www.ncbi.nlm.nih.gov/pubmed/28804508.
Anderson, R. E., M. L.
Sogin, et al. (2014). "Evolutionary strategies of viruses,
bacteria and archaea in hydrothermal vent ecosystems revealed
through metagenomics." PLoS One 9(10): e109696. http://www.ncbi.nlm.nih.gov/pubmed/25279954.
Arora, T. and R. Sharma
(2011). "Fermentation potential of the gut microbiome:
implications for energy homeostasis and weight management." Nutr
Rev 69(2):
99-106. http://www.ncbi.nlm.nih.gov/pubmed/21294743.
Arumugam, M., J. Raes,
et al. (2011). "Enterotypes of the human gut microbiome." Nature.
http://www.ncbi.nlm.nih.gov/pubmed/21508958.
Atanasova, N. S., M. K.
Pietila, et al. (2013). "Diverse antimicrobial interactions of
halophilic archaea and bacteria extend over geographical
distances and cross the domain barrier." Microbiologyopen
2(5): 811-825. http://www.ncbi.nlm.nih.gov/pubmed/23929527.
Aziz, R. K. (2009). "A
hundred-year-old insight into the gut microbiome!" Gut
Pathog 1(1):
21. http://www.ncbi.nlm.nih.gov/pubmed/19968883.
Berg, G., D. Rybakova,
et al. (2016). "The plant microbiome explored: implications
for experimental botany." J Exp Bot 67(4): 995-1002. http://www.ncbi.nlm.nih.gov/pubmed/26547794.
Berg Miller, M. E., C.
J. Yeoman, et al. (2012). "Phage-bacteria relationships and
CRISPR elements revealed by a metagenomic survey of the rumen
microbiome." Environ Microbiol 14(1): 207-227. http://www.ncbi.nlm.nih.gov/pubmed/22004549.
Boerner, B. P. and N. E.
Sarvetnick (2011). "Type 1 diabetes: role of intestinal
microbiome in humans and mice." Ann N Y Acad Sci 1243: 103-118. http://www.ncbi.nlm.nih.gov/pubmed/22211896.
Bordenstein, S. R. and
K. R. Theis (2015). "Host Biology in Light of the Microbiome:
Ten Principles of Holobionts and Hologenomes." PLoS Biol
13(8): e1002226. http://www.ncbi.nlm.nih.gov/pubmed/26284777.
Boyer, M., N. Yutin, et
al. (2009). "Giant Marseillevirus highlights the role of
amoebae as a melting pot in emergence of chimeric
microorganisms." Proc Natl Acad Sci U S A 106(51):
21848-21853. http://www.ncbi.nlm.nih.gov/pubmed/20007369.
Bultman, S. J. (2014).
"Emerging roles of the microbiome in cancer." Carcinogenesis
35(2): 249-255. http://www.ncbi.nlm.nih.gov/pubmed/24302613.
Caporaso, J. G., C. L.
Lauber, et al. (2011). "Moving pictures of the human
microbiome." Genome Biol 12(5): R50. http://www.ncbi.nlm.nih.gov/pubmed/21624126.
Cenit, M. C., V.
Matzaraki, et al. (2014). "Rapidly expanding knowledge on the
role of the gut microbiome in health and disease." Biochim
Biophys Acta. http://www.ncbi.nlm.nih.gov/pubmed/24882755.
Chen, Y. E., M. A.
Fischbach, et al. (2018). "Skin microbiota-host interactions."
Nature 553(7689):
427-436. http://www.ncbi.nlm.nih.gov/pubmed/29364286.
Cheng, X. Y., X. L.
Tian, et al. (2013). "Metagenomic analysis of the pinewood
nematode microbiome reveals a symbiotic relationship critical
for xenobiotics degradation." Sci Rep 3: 1869. http://www.ncbi.nlm.nih.gov/pubmed/23694939.
Cho, I., S. Yamanishi,
et al. (2012). "Antibiotics in early life alter the murine
colonic microbiome and adiposity." Nature. http://www.ncbi.nlm.nih.gov/pubmed/22914093.
Clemente, J. C. and M.
J. B. Erica C. Pehrsson, Kuldip Sandhu, Zhan Gao, Bin Wang,
Magda Magris, Glida Hidalgo, Monica Contreras, Óscar
Noya-Alarcón, Orlana Lander, Jeremy McDonald, Mike Cox, Jens
Walter, Phaik Lyn Oh, Jean F. Ruiz, Selena Rodriguez, Nan
Shen, Se Jin Song, Jessica Metcalf, Rob Knight, Gautam Dantas,
M. Gloria Dominguez-Bello (2015). "The microbiome of
uncontacted Amerindians." Science Advances 1(3): e1500183. .
Consortium, H. M.
(2012). "A framework for human microbiome research." Nature
486(7402):
215-221. http://www.ncbi.nlm.nih.gov/pubmed/22699610.
Consortium, H. M.
(2012). "Structure, function and diversity of the healthy
human microbiome." Nature 486(7402): 207-214.
http://www.ncbi.nlm.nih.gov/pubmed/22699609.
Cryan, J. F. and S. M.
O'Mahony (2011). "The microbiome-gut-brain axis: from bowel to
behavior." Neurogastroenterol Motil 23(3): 187-192. http://www.ncbi.nlm.nih.gov/pubmed/21303428.
Dash, S., G. Clarke, et
al. (2015). "The gut microbiome and diet in psychiatry: focus
on depression." Curr Opin Psychiatry 28(1): 1-6. http://www.ncbi.nlm.nih.gov/pubmed/25415497.
Davenport, E. R., J. G.
Sanders, et al. (2017). "The human microbiome in evolution." BMC
Biol 15(1):
127. http://www.ncbi.nlm.nih.gov/pubmed/29282061.
Diaz-Munoz, S. L., A. M.
Boddy, et al. (2016). "Contextual organismality: Beyond
pattern to process in the emergence of organisms." Evolution
70(12): 2669-2677.
http://www.ncbi.nlm.nih.gov/pubmed/27704542.
Doerflinger, S. Y., A.
L. Throop, et al. (2014). "Bacteria in the vaginal microbiome
alter the innate immune response and barrier properties of the
human vaginal epithelia in a species-specific manner." J
Infect Dis 209(12):
1989-1999. http://www.ncbi.nlm.nih.gov/pubmed/24403560.
Donia, M. S., P.
Cimermancic, et al. (2014). "A systematic analysis of
biosynthetic gene clusters in the human microbiome reveals a
common family of antibiotics." Cell 158(6): 1402-1414. http://www.ncbi.nlm.nih.gov/pubmed/25215495.
Edgcomb, V. P., E. R.
Leadbetter, et al. (2011). "Structured multiple endosymbiosis
of bacteria and archaea in a ciliate from marine sulfidic
sediments: a survival mechanism in low oxygen, sulfidic
sediments?" Front Microbiol 2: 55. http://www.ncbi.nlm.nih.gov/pubmed/21833311.
Edwards, J., C. Johnson,
et al. (2015). "Structure, variation, and assembly of the
root-associated microbiomes of rice." Proc Natl Acad Sci U
S A 112(8):
E911-920. http://www.ncbi.nlm.nih.gov/pubmed/25605935.
Ellrott, K., L.
Jaroszewski, et al. (2010). "Expansion of the protein
repertoire in newly explored environments: human gut
microbiome specific protein families." PLoS Comput Biol
6(6): e1000798. http://www.ncbi.nlm.nih.gov/pubmed/20532204.
Garcia-Bonilla, E., P.
F. B. Brandao, et al. (2018). "Stable and Enriched Cenarchaeum
symbiosum and Uncultured Betaproteobacteria HF1 in the
Microbiome of the Mediterranean Sponge Haliclona fulva
(Demospongiae: Haplosclerida)." Microb Ecol. http://www.ncbi.nlm.nih.gov/pubmed/29766224.
Gevers, D., R. Knight,
et al. (2012). "The human microbiome project: a community
resource for the healthy human microbiome." PLoS Biol
10(8): e1001377. http://www.ncbi.nlm.nih.gov/pubmed/22904687.
Gilbert, S. F. (2014).
"A holobiont birth narrative: the epigenetic transmission of
the human microbiome." Front Genet 5: 282. http://www.ncbi.nlm.nih.gov/pubmed/25191338.
Gill, S. R., M. Pop, et
al. (2006). "Metagenomic analysis of the human distal gut
microbiome." Science 312(5778):
1355-1359. http://www.ncbi.nlm.nih.gov/pubmed/16741115.
Gomez-Valero, L. and C.
Buchrieser (2013). "Genome dynamics in Legionella: the basis
of versatility and adaptation to intracellular replication." Cold
Spring Harb Perspect Med 3(6). http://www.ncbi.nlm.nih.gov/pubmed/23732852.
Goodrich, J. K., J. L.
Waters, et al. (2014). "Human genetics shape the gut
microbiome." Cell 159(4): 789-799. http://www.ncbi.nlm.nih.gov/pubmed/25417156.
Gopalakrishnan, V., C.
N. Spencer, et al. (2018). "Gut microbiome modulates response
to anti-PD-1 immunotherapy in melanoma patients." Science
359(6371): 97-103.
http://www.ncbi.nlm.nih.gov/pubmed/29097493.
Grice, E. A., H. H.
Kong, et al. (2009). "Topographical and temporal diversity of
the human skin microbiome." Science 324(5931):
1190-1192. http://www.ncbi.nlm.nih.gov/pubmed/19478181.
Grice, E. A. and J. A.
Segre (2011). "The skin microbiome." Nat Rev Microbiol
9(4): 244-253. http://www.ncbi.nlm.nih.gov/pubmed/21407241.
Grice, E. A. and J. A.
Segre (2012). "The human microbiome: our second genome." Annu
Rev Genomics Hum Genet 13: 151-170. http://www.ncbi.nlm.nih.gov/pubmed/22703178.
Guerrero, R., L.
Margulis, et al. (2013). "Symbiogenesis: the holobiont as a
unit of evolution." Int Microbiol 16(3): 133-143. http://www.ncbi.nlm.nih.gov/pubmed/24568029.
Guimaraes, A. J., K. X.
Gomes, et al. (2016). "Acanthamoeba spp. as a universal host
for pathogenic microorganisms: One bridge from environment to
host virulence." Microbiol Res 193: 30-38. http://www.ncbi.nlm.nih.gov/pubmed/27825484.
Hamady, M. and R. Knight
(2009). "Microbial community profiling for human microbiome
projects: Tools, techniques, and challenges." Genome Res
19(7): 1141-1152.
http://www.ncbi.nlm.nih.gov/pubmed/19383763.
Hasegawa, Y., J. L. Mark
Welch, et al. (2017). "Preservation of three-dimensional
spatial structure in the gut microbiome." PLoS One 12(11): e0188257. http://www.ncbi.nlm.nih.gov/pubmed/29176788.
Hentschel, U., J. Piel,
et al. (2012). "Genomic insights into the marine sponge
microbiome." Nat Rev Microbiol 10(9): 641-654. http://www.ncbi.nlm.nih.gov/pubmed/22842661.
Hoban, A. E., R. M.
Stilling, et al. (2017). "The microbiome regulates
amygdala-dependent fear recall." Mol Psychiatry. http://www.ncbi.nlm.nih.gov/pubmed/28507320.
Hoffmann, C., C. F.
Harrison, et al. (2014). "The natural alternative: protozoa as
cellular models for Legionella infection." Cell Microbiol
16(1): 15-26. http://www.ncbi.nlm.nih.gov/pubmed/24168696.
Ivens, A. B. F., A.
Gadau, et al. (2018). "Can social partnerships influence the
microbiome? Insights from ant farmers and their trophobiont
mutualists." Mol Ecol 27(8): 1898-1914. http://www.ncbi.nlm.nih.gov/pubmed/29411455.
Jakobsson, H. E., C.
Jernberg, et al. (2010). "Short-term antibiotic treatment has
differing long-term impacts on the human throat and gut
microbiome." PLoS One 5(3): e9836. http://www.ncbi.nlm.nih.gov/pubmed/20352091.
Jin, W., Y. Li, et al.
(2018). "The bacterial and archaeal community structures and
methanogenic potential of the cecal microbiota of goats fed
with hay and high-grain diets." Antonie Van Leeuwenhoek.
http://www.ncbi.nlm.nih.gov/pubmed/29774508.
Johnson, K. V. and K. R.
Foster (2018). "Why does the microbiome affect behaviour?" Nat
Rev Microbiol 16(10):
647-655. http://www.ncbi.nlm.nih.gov/pubmed/29691482.
Jones, B. V., F. Sun, et
al. (2010). "Comparative metagenomic analysis of plasmid
encoded functions in the human gut microbiome." BMC
Genomics 11:
46. http://www.ncbi.nlm.nih.gov/pubmed/20085629.
Kim, B. S., Y. S. Jeon,
et al. (2013). "Current status and future promise of the human
microbiome." Pediatr Gastroenterol Hepatol Nutr 16(2): 71-79. http://www.ncbi.nlm.nih.gov/pubmed/24010110.
Kinross, J. M., A. W.
Darzi, et al. (2011). "Gut microbiome-host interactions in
health and disease." Genome Med 3(3): 14. http://www.ncbi.nlm.nih.gov/pubmed/21392406.
Koren, O., J. K.
Goodrich, et al. (2012). "Host Remodeling of the Gut
Microbiome and Metabolic Changes during Pregnancy." Cell
150(3): 470-480. http://www.ncbi.nlm.nih.gov/pubmed/22863002.
Koskella, B., L. J.
Hall, et al. (2017). "The microbiome beyond the horizon of
ecological and evolutionary theory." Nat Ecol Evol. http://www.ncbi.nlm.nih.gov/pubmed/29038487.
Koskinen, K., M. R.
Pausan, et al. (2017). "First Insights into the Diverse Human
Archaeome: Specific Detection of Archaea in the
Gastrointestinal Tract, Lung, and Nose and on Skin." MBio
8(6). http://www.ncbi.nlm.nih.gov/pubmed/29138298.
Kuczynski, J., E. K.
Costello, et al. (2010). "Direct sequencing of the human
microbiome readily reveals community differences." Genome
Biol 11(5):
210. http://www.ncbi.nlm.nih.gov/pubmed/20441597.
Kundu, P., E. Blacher,
et al. (2017). "Our Gut Microbiome: The Evolving Inner Self."
Cell 171(7):
1481-1493. http://www.ncbi.nlm.nih.gov/pubmed/29245010.
Lagier, J. C., F.
Armougom, et al. (2012). "Microbial culturomics: paradigm
shift in the human gut microbiome study." Clin Microbiol
Infect 18(12):
1185-1193. http://www.ncbi.nlm.nih.gov/pubmed/23033984.
Lebeis, S. L., S. H.
Paredes, et al. (2015). "Salicylic acid modulates colonization
of the root microbiome by specific bacterial taxa." Science.
http://www.ncbi.nlm.nih.gov/pubmed/26184915.
Lepage, P., M. C.
Leclerc, et al. (2013). "A metagenomic insight into our gut's
microbiome." Gut 62(1): 146-158. http://www.ncbi.nlm.nih.gov/pubmed/22525886.
Li, J., H. Jia, et al.
(2014). "An integrated catalog of reference genes in the human
gut microbiome." Nat Biotechnol 32(8): 834-841. http://www.ncbi.nlm.nih.gov/pubmed/24997786.
Liu, H., L. C.
Carvalhais, et al. (2017). "Effects of jasmonic acid
signalling on the wheat microbiome differ between body sites."
Sci Rep 7:
41766. http://www.ncbi.nlm.nih.gov/pubmed/28134326.
Looft, T. and H. K.
Allen (2012). "Collateral effects of antibiotics on mammalian
gut microbiomes." Gut Microbes 3(5): 463-467. http://www.ncbi.nlm.nih.gov/pubmed/22825498.
Lundberg, D. S., S. L.
Lebeis, et al. (2012). "Defining the core Arabidopsis thaliana
root microbiome." Nature 488(7409): 86-90. http://www.ncbi.nlm.nih.gov/pubmed/22859206.
Margulis, L. (1991).
Symbiogenesis and symbionticism. Symbiosis as a source of
evolutionary innovation: speciation and morphogenesis.
L. Margulis and R. Fester. Canbridge USA, MIT Press: 49-92. .
Matson, V., J. Fessler,
et al. (2018). "The commensal microbiome is associated with
anti-PD-1 efficacy in metastatic melanoma patients." Science
359(6371):
104-108. http://www.ncbi.nlm.nih.gov/pubmed/29302014.
Moissl-Eichinger, C., M.
Pausan, et al. (2018). "Archaea Are Interactive Components of
Complex Microbiomes." Trends Microbiol 26(1): 70-85. http://www.ncbi.nlm.nih.gov/pubmed/28826642.
Moissl-Eichinger, C., A.
J. Probst, et al. (2017). "Human age and skin physiology shape
diversity and abundance of Archaea on skin." Sci Rep 7(1): 4039. http://www.ncbi.nlm.nih.gov/pubmed/28642547.
Moliner, C., P. E.
Fournier, et al. (2010). "Genome analysis of microorganisms
living in amoebae reveals a melting pot of evolution." FEMS
Microbiol Rev 34(3):
281-294. http://www.ncbi.nlm.nih.gov/pubmed/20132312.
Morowitz, M. J., T.
Babrowski, et al. (2011). "The human microbiome and surgical
disease." Ann Surg 253(6): 1094-1101. http://www.ncbi.nlm.nih.gov/pubmed/21422915.
Murillo-Rincon, A. P.,
A. Klimovich, et al. (2017). "Spontaneous body contractions
are modulated by the microbiome of Hydra." Sci Rep 7(1): 15937. http://www.ncbi.nlm.nih.gov/pubmed/29162937.
Nelson, K. E., G. M.
Weinstock, et al. (2010). "A catalog of reference genomes from
the human microbiome." Science 328(5981): 994-999.
http://www.ncbi.nlm.nih.gov/pubmed/20489017.
Panke-Buisse, K., A. C.
Poole, et al. (2015). "Selection on soil microbiomes reveals
reproducible impacts on plant function." ISME J 9(4): 980-989. http://www.ncbi.nlm.nih.gov/pubmed/25350154.
Parfrey, L. W., W. A.
Walters, et al. (2011). "Microbial eukaryotes in the human
microbiome: ecology, evolution, and future directions." Front
Microbiol 2:
153. http://www.ncbi.nlm.nih.gov/pubmed/21808637.
Passos da Silva, D., M.
P. Castaneda-Ojeda, et al. (2014). "Bacterial multispecies
studies and microbiome analysis of a plant disease." Microbiology
160(Pt 3): 556-566.
http://www.ncbi.nlm.nih.gov/pubmed/24421406.
Peixoto, R. J. M., E. S.
Alves, et al. (2017). "Repression of Salmonella host cell
invasion by aromatic small molecules from the human fecal
metabolome." Appl Environ Microbiol. http://www.ncbi.nlm.nih.gov/pubmed/28754707.
Perez-Jaramillo, J. E.,
V. J. Carrion, et al. (2017). "Linking rhizosphere microbiome
composition of wild and domesticated Phaseolus vulgaris to
genotypic and root phenotypic traits." ISME J 11(10): 2244-2257. http://www.ncbi.nlm.nih.gov/pubmed/28585939.
Peterson, J., S. Garges,
et al. (2009). "The NIH Human Microbiome Project." Genome
Res 19(12):
2317-2323. http://www.ncbi.nlm.nih.gov/pubmed/19819907.
Piewngam, P., Y. Zheng,
et al. (2018). "Pathogen elimination by probiotic Bacillus via
signalling interference." Nature. http://www.ncbi.nlm.nih.gov/pubmed/30305736.
Pinto, C., D. Pinho, et
al. (2014). "Unravelling the diversity of grapevine
microbiome." PLoS One 9(1): e85622. http://www.ncbi.nlm.nih.gov/pubmed/24454903.
Pita, L., L. Rix, et al.
(2018). "The sponge holobiont in a changing ocean: from
microbes to ecosystems." Microbiome 6(1): 46. http://www.ncbi.nlm.nih.gov/pubmed/29523192.
Raymann, K. and N. A.
Moran (2018). "The role of the gut microbiome in health and
disease of adult honey bee workers." Curr Opin Insect Sci
26: 97-104. http://www.ncbi.nlm.nih.gov/pubmed/29764668.
Rees, T., T. Bosch, et
al. (2018). "How the microbiome challenges our concept of
self." PLoS Biol 16(2): e2005358. http://www.ncbi.nlm.nih.gov/pubmed/29425197.
Romano-Keeler, J., J. H.
Weitkamp, et al. (2012). "Regulatory properties of the
intestinal microbiome effecting the development and treatment
of diabetes." Curr Opin Endocrinol Diabetes Obes 19(2): 73-80. http://www.ncbi.nlm.nih.gov/pubmed/22357099.
Rosenberg, E. and I.
Zilber-Rosenberg (2016). "Microbes Drive Evolution of Animals
and Plants: the Hologenome Concept." MBio 7(2): e01395. http://www.ncbi.nlm.nih.gov/pubmed/27034283.
Rosenberg, E. and I.
Zilber-Rosenberg (2018). "The hologenome concept of evolution
after 10 years." Microbiome 6(1): 78. http://www.ncbi.nlm.nih.gov/pubmed/29695294.
Salvucci, E. (2014).
"Microbiome, holobiont and the net of life." Crit Rev
Microbiol: 1-10. http://www.ncbi.nlm.nih.gov/pubmed/25430522.
Sandoval-Motta, S., M.
Aldana, et al. (2018). "Evolving Ecosystems: Inheritance and
Selection in the Light of the Microbiome." Arch Med Res.
http://www.ncbi.nlm.nih.gov/pubmed/29366516.
Schwabe, R. F. and C.
Jobin (2013). "The microbiome and cancer." Nat Rev Cancer
13(11): 800-812. http://www.ncbi.nlm.nih.gov/pubmed/24132111.
Shin, S. C., S. H. Kim,
et al. (2011). "Drosophila microbiome modulates host
developmental and metabolic homeostasis via insulin
signaling." Science 334(6056): 670-674. http://www.ncbi.nlm.nih.gov/pubmed/22053049.
Shropshire, J. D. and S.
R. Bordenstein (2016). "Speciation by Symbiosis: the
Microbiome and Behavior." MBio 7(2). http://www.ncbi.nlm.nih.gov/pubmed/27034284.
Shterzer, N. and I.
Mizrahi (2015). "The animal gut as a melting pot for
horizontal gene transfer." Can J Microbiol 61(9): 603-605. http://www.ncbi.nlm.nih.gov/pubmed/26053634.
Six, D. L. (2013). "The
bark beetle holobiont: why microbes matter." J Chem Ecol
39(7): 989-1002. http://www.ncbi.nlm.nih.gov/pubmed/23846183.
Smillie, C. S., M. B.
Smith, et al. (2011). "Ecology drives a global network of gene
exchange connecting the human microbiome." Nature 480(7376): 241-244.
http://www.ncbi.nlm.nih.gov/pubmed/22037308.
Smith, M. I., T.
Yatsunenko, et al. (2013). "Gut microbiomes of Malawian twin
pairs discordant for kwashiorkor." Science 339(6119): 548-554.
http://www.ncbi.nlm.nih.gov/pubmed/23363771.
Snyder, A. K. and R. V.
Rio (2013). "Interwoven biology of the tsetse holobiont." J
Bacteriol 195(19):
4322-4330. http://www.ncbi.nlm.nih.gov/pubmed/23836873.
Stams, A. J. and C. M.
Plugge (2009). "Electron transfer in syntrophic communities of
anaerobic bacteria and archaea." Nat Rev Microbiol 7(8): 568-577. http://www.ncbi.nlm.nih.gov/pubmed/19609258.
Stolz, J. F. (2017).
"Gaia and her microbiome." FEMS Microbiol Ecol 93(2). http://www.ncbi.nlm.nih.gov/pubmed/27940647.
Suen, G., J. J. Scott,
et al. (2010). "An insect herbivore microbiome with high plant
biomass-degrading capacity." PLoS Genet 6(9). http://www.ncbi.nlm.nih.gov/pubmed/20885794.
Sunagawa, S., L. P.
Coelho, et al. (2015). "Ocean plankton. Structure and function
of the global ocean microbiome." Science 348(6237): 1261359.
http://www.ncbi.nlm.nih.gov/pubmed/25999513.
Theis, K. R., N. M.
Dheilly, et al. (2016). "Getting the Hologenome Concept Right:
an Eco-Evolutionary Framework for Hosts and Their
Microbiomes." mSystems 1(2). http://www.ncbi.nlm.nih.gov/pubmed/27822520.
Thompson, J. R., H. E.
Rivera, et al. (2014). "Microbes in the coral holobiont:
partners through evolution, development, and ecological
interactions." Front Cell Infect Microbiol 4: 176. http://www.ncbi.nlm.nih.gov/pubmed/25621279.
Tilg, H. and A. Kaser
(2011). "Gut microbiome, obesity, and metabolic dysfunction."
J Clin Invest 121(6):
2126-2132. http://www.ncbi.nlm.nih.gov/pubmed/21633181.
Tropini, C., K. A.
Earle, et al. (2017). "The Gut Microbiome: Connecting Spatial
Organization to Function." Cell Host Microbe 21(4): 433-442. http://www.ncbi.nlm.nih.gov/pubmed/28407481.
Turnbaugh, P. J. and J.
I. Gordon (2009). "The core gut microbiome, energy balance and
obesity." J Physiol 587(Pt 17):
4153-4158. http://www.ncbi.nlm.nih.gov/pubmed/19491241.
van de Water, J., D.
Allemand, et al. (2018). "Host-microbe interactions in
octocoral holobionts - recent advances and perspectives." Microbiome
6(1): 64. http://www.ncbi.nlm.nih.gov/pubmed/29609655.
Vandenkoornhuyse, P., A.
Quaiser, et al. (2015). "The importance of the microbiome of
the plant holobiont." New Phytol 206(4): 1196-1206. http://www.ncbi.nlm.nih.gov/pubmed/25655016.
Vindigni, S. M., E. K.
Broussard, et al. (2013). "Alteration of the intestinal
microbiome: fecal microbiota transplant and probiotics for
Clostridium difficile and beyond." Expert Rev
Gastroenterol Hepatol 7(7): 615-628. http://www.ncbi.nlm.nih.gov/pubmed/24070153.
Wang, Z. and M. Wu
(2017). "Comparative Genomic Analysis of Acanthamoeba
Endosymbionts Highlights the Role of Amoebae as a "Melting
Pot" Shaping the Rickettsiales Evolution." Genome Biol
Evol 9(11):
3214-3224. http://www.ncbi.nlm.nih.gov/pubmed/29177480.
Wegener, G., V.
Krukenberg, et al. (2015). "Intercellular wiring enables
electron transfer between methanotrophic archaea and
bacteria." Nature 526(7574): 587-590.
http://www.ncbi.nlm.nih.gov/pubmed/26490622.
Weinstock, G. M. (2011).
"The volatile microbiome." Genome Biol 12(5): 114. http://www.ncbi.nlm.nih.gov/pubmed/21635714.
Weiss, B. L., J. Wang,
et al. (2013). "Trypanosome infection establishment in the
tsetse fly gut is influenced by microbiome-regulated host
immune barriers." PLoS Pathog 9(4): e1003318. http://www.ncbi.nlm.nih.gov/pubmed/23637607.
Wrede, C., A. Dreier, et
al. (2012). "Archaea in symbioses." Archaea 2012: 596846. http://www.ncbi.nlm.nih.gov/pubmed/23326206.
Wylie, K. M., R. M.
Truty, et al. (2012). "Novel bacterial taxa in the human
microbiome." PLoS One 7(6): e35294. http://www.ncbi.nlm.nih.gov/pubmed/22719826.
Yang, X., L. Xie, et al.
(2009). "More than 9,000,000 unique genes in human gut
bacterial community: estimating gene numbers inside a human
body." PLoS One 4(6): e6074. http://www.ncbi.nlm.nih.gov/pubmed/19562079.
Ye, Y. (2014).
"Identification of diversity-generating retroelements in human
microbiomes." Int J Mol Sci 15(8): 14234-14246.
http://www.ncbi.nlm.nih.gov/pubmed/25196521.
Yousuf, F. A., R.
Siddiqui, et al. (2013). "Acanthamoeba castellanii of the T4
genotype is a potential environmental host for Enterobacter
aerogenes and Aeromonas hydrophila." Parasit Vectors 6: 169. http://www.ncbi.nlm.nih.gov/pubmed/23742105.
Zarraonaindia, I., S. M.
Owens, et al. (2015). "The soil microbiome influences
grapevine-associated microbiota." MBio 6(2). http://www.ncbi.nlm.nih.gov/pubmed/25805735.
Zhu, B., X. Wang, et al.
(2010). "Human gut microbiome: the second genome of human
body." Protein Cell 1(8): 718-725. http://www.ncbi.nlm.nih.gov/pubmed/21203913.
Zhu, L., W. Liu, et al.
(2014). "Structural changes in the gut microbiome of
constipated patients." Physiol Genomics. http://www.ncbi.nlm.nih.gov/pubmed/25073603.
Zitvogel, L., Y. Ma, et
al. (2018). "The microbiome in cancer immunotherapy:
Diagnostic tools and therapeutic strategies." Science
359(6382):
1366-1370. http://www.ncbi.nlm.nih.gov/pubmed/29567708.
Zrzavy, J. and Z. Skala
(1993). "Holobionts, hybrids, and cladistic classification." Biosystems
31(2-3): 127-130;
discussion 130-123. http://www.ncbi.nlm.nih.gov/pubmed/8155845.