266:) are commonly utilized to compare multiple traits across organisms. Within the scope of microbiome studies, it is not common for the use of PCMs, however, recent studies have been successful in identifying genes associated with colonization of human gut. This challenge was addressed through measuring the statistical association between a species that harbors the gene and the probability the species is present in the gut microbiome. The analyses showcase the combination of shotgun metagenomics paired with phylogenetically aware models.
287:
carrying biological information. Recent methods such as PhILR and phylofactorization address the challenges of phylogenetic variables analysis. The PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges. Incorporating both microbial evolutionary models with the isometric log-ratio transform creates the PhILR transform. Phylofactorization is a dimensionality-reducing tool used to identify edges in the phylogeny from which putative functional ecological traits may have arisen.
1824:
2391:
278:(Phylogenetic Investigation of Communities by Reconstructing of Unobserved States) in microbiome studies. PICRUSt is a computational approach capable of prediction functional composition of a metagenome with marker data and a database of reference genomes. To predict which gene families are present, PICRUSt uses extended ancestral-state reconstruction algorithm and then combines the gene families to estimate composite metagenome.
221:
some evolutionary microbiologists suggested abandoning this classical view in favor of a representation of genealogies more closely resembling a web, also known as network. However, there are some issues with this network representation, such as the inability to precisely establish the donor organism
286:
Phylogenetic variables are used to describe variables that are constructed using features in the phylogeny to summarize and contrast data of species in the phylogenetic tree. Microbiome datasets can be simplifies using phylogenetic variables by reducing the dimensions of the data to a few variables
295:
Inferences in phylogenetics requires the assumption of common ancestry or homology but when this assumption is violated the signal can be disrupted by noise. It is possible for microbial traits to be unrelated due to horizontal gene transfer causing the taxonomic composition to reveal little about
94:(16rRNA) oligonucleotides. Matching oligonucleotides in different bacteria could be compared to one another to determine how closely the organisms were related. In 1977, after collecting and comparing 16s rRNA fragments for almost 200 species of bacteria,
238:
are essential tools for organizing the diversity of life. Collecting gene sequences, aligning such sequences based on homologies and thus using models of mutation to infer evolutionary history are common methods to estimate microbial phylogenies.
222:
for a HGT event and the difficulty to determine the correct path across organisms when multiple HGT events happened. Therefore, there is not still a consensus between biologists on which representation is a better fit for the microbial world.
1505:
Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega
Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis (2013).
253:
Phylogenetic inferences are determined based on the genes chosen, for example, 16S rRNA gene is commonly selected to investigate inferences in
Bacteria and Archaea, and microbial eukaryotes most commonly use the 18S RNA gene.
157:
In the late 1990s sequencing of genomes from various microbial organisms started and by 2005, 260 complete genomes had been sequenced resulting in the classification of 33 eucaryotes, 206 eubacteria, and 21 archeons.
126:
was facilitated by the development of the means to clone DNA, making possible to create many copies of sequences from minute samples. Of incredible impact for the microbial phylogenetics was the invention of the
150:
genes obtained from DNA isolated directly from the environment. This technique made possible to fully appreciate that bacteria, not only to have the greatest diversity but to constitute the greatest
146:
One of the intrinsic problems of studying microbial organisms was the dependence of the studies from pure culture in a laboratory. Biologists tried to overcome this limitation by sequencing
178:
differed greatly from the ones based on the rRNA. These gene histories were so different between them that the only hypothesis that could explain these divergences was a major influence of
1622:
Washburne, Alex D.; Silverman, Justin D.; Leff, Jonathan W.; Bennett, Dominic J.; Darcy, John L.; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A. (2017-02-09).
274:
This method is commonly used for estimation of genetic and metabolic profiles of extant communities using a set of reference genomes, commonly performed with
143:(Woese himself proposed this name to replace the old nomination of Archaebacteria), and Eukarya, arguably one of the key passage in the history of taxonomy.
2032:
2371:
2361:
1748:
2147:
2122:
1274:
Washburne, Alex D.; Morton, James T.; Sanders, Jon; McDonald, Daniel; Zhu, Qiyun; Oliverio, Angela M.; Knight, Rob (2018-05-24).
771:
402:
373:
2168:
456:
Dietrich, M. (1998). "Paradox and persuasion: Negotiating the place of molecular evolution within evolutionary biology".
213:, every phylogeny for every organism has been represented in the form of a tree. Nonetheless, due to the great role that
2356:
960:
719:
Mullis, K.F.; et al. (1986). "Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction".
249:(SSU rRNA) have revolutionized microbial classification since the 1970s and has since become the most sequenced gene
197:
Studies aimed at understanding the widespread of HGT suggested that the ease with which genes are transferred among
2425:
2183:
2163:
1128:
Ochman, H.; Lawrence, J.G.; Groisman, E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation".
263:
194:
have to be carefully studied before being used as a measure of genealogical relationship for microbial organisms.
1053:
330:
2267:
2132:
1865:
1823:
1741:
1624:"Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets"
2208:
325:
2238:
2127:
1953:
1925:
315:
128:
2257:
1968:
214:
179:
1448:"Phylogeny-corrected identification of microbial gene families relevant to human gut colonization"
2420:
2394:
2308:
2303:
2198:
2112:
1734:
335:
789:"Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya"
2415:
2349:
2293:
1850:
1840:
1508:"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences"
394:
365:
1181:"Horizontal gene transfer among microbial genomes: new insights from complete genome analysis"
2339:
2283:
2188:
2087:
1963:
1896:
881:
Pace, N.R.; et al. (1985). "Analyzing natural microbial populations by rRNA sequences".
119:
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from a completely unrelated organism. HGT explains why similarities and differences in some
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1958:
1855:
1137:
913:
800:
673:
614:
555:
305:
31:
1681:
Martiny, Jennifer B. H.; Jones, Stuart E.; Lennon, Jay T.; Martiny, Adam C. (2015-11-06).
1563:
Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A (2017-02-15).
230:
Most microbial taxa have never been cultivated or experimentally characterized. Utilizing
8:
2061:
39:
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804:
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767:
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642:
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369:
151:
110:
In the 1980s microbial phylogenetics went into its golden age, as the techniques for
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1315:
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995:
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2051:
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508:
465:
430:
132:
1022:
528:
2218:
2102:
2056:
1948:
1464:
859:
499:
Dietrich, M. (1994). "The origins of the neutral theory of molecular evolution".
732:
434:
166:
In the early 2000s, scientists started creating phylogenetic trees based not on
90:
instead of proteins. More specifically, he decided to compare the small subunit
2334:
2329:
2288:
2213:
2092:
2027:
1988:
1978:
210:
171:
111:
1350:
1291:
1009:
Doolittle, W.F. (1999). "Phylogenetic classification and the universal tree".
469:
2409:
2233:
2178:
2142:
2000:
1793:
1783:
1765:
1757:
1708:
1649:
1590:
1565:"A phylogenetic transform enhances analysis of compositional microbiota data"
1531:
1473:
1416:
1359:
1299:
1096:
846:
Pace, N (1997). "A molecular view of microbial diversity and the biosphere".
340:
310:
218:
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147:
91:
56:
23:
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627:
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1832:
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1667:
1608:
1549:
1491:
1446:
Bradley, Patrick H.; Nayfach, Stephen; Pollard, Katherine S. (2018-08-09).
1377:
1307:
1253:
1204:
1157:
1114:
1030:
987:
520:
477:
442:
170:, but on other genes with different function (for example the gene for the
1424:
945:
867:
832:
740:
686:
2376:
2137:
1993:
705:
646:
587:
60:
1581:
131:(PCR). All these new techniques led to the formal proposal of the three
2228:
2107:
2015:
2010:
1798:
1640:
1235:
544:"Phylogenetic structure of the procaryote domain: The primary kingdoms"
512:
95:
79:
72:
64:
59:
emerged as a field of study in the 1960s, scientists started to create
35:
1071:"Biased gene transfer mimics patterns created through shared ancestry"
78:
One of the most important figures in the early stage of this field is
2203:
2020:
1523:
1149:
235:
175:
27:
1220:"The net of life: Reconstructing the microbial phylogenetic network"
1069:
Andam, Cheryl P.; Williams, David; Gogarten, J. Peter (2010-06-08).
979:
201:
made impossible to apply ‘the biological species concept’ for them.
2313:
1875:
1870:
1808:
1778:
1408:
421:
Sapp, J. (2007). "The structure of microbial evolutionary theory".
281:
240:
231:
198:
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1943:
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Kunin, V.; Goldovsky, L.; Darzentas, N.; Ouzounis, C. A. (2005).
275:
140:
99:
68:
1562:
1504:
102:
were not part of
Bacteria but completely independent organisms.
1788:
1393:"Ribosomal DNA: Molecular Evolution and Phylogenetic Inference"
1334:"A simple, fast, and accurate method of phylogenomic inference"
1217:
1273:
225:
75:
of genes instead of using comparative anatomy and physiology.
2366:
1813:
1621:
1683:"Microbiomes in light of traits: A phylogenetic perspective"
191:
187:
123:
961:"Phylogenomics and the reconstruction of the tree of life"
1680:
115:
87:
958:
1276:"Methods for phylogenetic analysis of microbiome data"
1127:
22:
is the study of the manner in which various groups of
1445:
1068:
600:
721:
Cold Spring Harbor
Symposia on Quantitative Biology
257:
26:are genetically related. This helps to trace their
603:"DNA sequencing with chain-terminating inhibitors"
30:. To study these relationships biologists rely on
1048:. New York: Cold Spring Harbor Laboratory Press.
1046:Lateral DNA transfer: mechanisms and consequences
269:
118:improved greatly. For example, comparison of the
2407:
959:Delusc, F.; Brinkmann, H.; Philippe, H. (2005).
282:Analysis of phylogenetic variables and distances
1075:Proceedings of the National Academy of Sciences
906:Proceedings of the National Academy of Sciences
793:Proceedings of the National Academy of Sciences
666:Proceedings of the National Academy of Sciences
607:Proceedings of the National Academy of Sciences
601:Sanger, F.; Nicklen, S.; Coulson, A.R. (1977).
548:Proceedings of the National Academy of Sciences
204:
1742:
1185:Current Opinion in Genetics & Development
761:
1391:Hillis, David M.; Dixon, Michael T. (1991).
1390:
391:Archaea: New Models for Prokaryotic Biology
226:Methods for Microbial Phylogenetic Analysis
1749:
1735:
2372:Physical factors affecting microbial life
2362:Microbially induced sedimentary structure
1698:
1657:
1639:
1598:
1580:
1539:
1481:
1463:
1367:
1349:
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1008:
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925:
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812:
695:
685:
636:
626:
577:
567:
423:Stud. Hist. Phil. Biol. & Biomed. Sci
541:
498:
455:
2148:International Census of Marine Microbes
2123:Hydrothermal vent microbial communities
1331:
1043:
899:
388:
359:
2408:
1332:Wu, Martin; Eisen, Jonathan A (2008).
718:
1730:
1327:
1325:
1269:
1267:
1265:
1263:
1178:
883:American Society of Microbiology News
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659:
362:Molecular Phylogeny of Microorganisms
63:based on differences in the order of
2169:Microbiomes of the built environment
880:
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766:. Academic Press. pp. 189–204.
762:Mullis, K.B.; Faloona, F.A. (1989).
420:
416:
414:
353:
98:and his team in 1977 concluded that
82:, who in his researches, focused on
900:Whitman, W. B; et al. (1998).
382:
182:(HGT), a mechanism which permits a
13:
2357:Lines on the Antiquity of Microbes
1756:
1322:
1260:
902:"Procaryotes: The unseen majority"
262:Phylogenetic comparative methods (
14:
2437:
787:Woese, C.R.; et al. (1990).
662:"A new method for sequencing DNA"
501:Journal of the History of Biology
458:Journal of the History of Biology
411:
360:Oren, A (2010). Papke, RT (ed.).
2390:
2389:
2184:Microbial symbiosis and immunity
1822:
258:Phylogenetic comparative methods
1674:
1615:
1556:
1498:
1439:
1397:The Quarterly Review of Biology
1384:
1211:
1172:
1121:
1062:
1037:
1002:
952:
893:
874:
839:
780:
755:
542:Woese, C.R.; Fox, G.E. (1977).
712:
653:
594:
535:
492:
449:
331:History of molecular evolution
270:Ancestral state reconstruction
105:
50:
1:
2268:Synthetic microbial consortia
2133:Microbial oxidation of sulfur
2033:Host microbe interactions in
1197:10.1016/S0959-437X(00)00143-X
1023:10.1126/science.284.5423.2124
346:
290:
1866:Microbial population biology
1465:10.1371/journal.pcbi.1006242
860:10.1126/science.276.5313.734
7:
764:Recombinant DNA Methodology
733:10.1101/SQB.1986.051.01.032
435:10.1016/j.shpsc.2007.09.011
326:Computational phylogenetics
299:
205:Phylogenetic representation
10:
2442:
2128:Marine microbial symbiosis
1954:Kill the Winner hypothesis
1926:Bacteria collective motion
1452:PLOS Computational Biology
316:Multilocus sequence typing
296:the function of a system.
45:
42:are not possible methods.
2385:
2322:
2276:
2164:Microbes in human culture
2156:
2080:
2044:
1934:
1884:
1831:
1820:
1764:
1351:10.1186/gb-2008-9-10-r151
1292:10.1038/s41564-018-0156-0
129:polymerase chain reaction
2258:Human Microbiome Project
1969:Microbial biodegradation
180:horizontal gene transfer
161:
2426:Eukaryotic microbiology
2309:Microbiological culture
2304:Microbial DNA barcoding
2113:Antarctic microorganism
1861:Microbial phylogenetics
1700:10.1126/science.aac9323
1088:10.1073/pnas.1001418107
968:Nature Reviews Genetics
927:10.1073/pnas.95.12.6578
814:10.1073/pnas.87.12.4576
628:10.1073/pnas.74.12.5463
569:10.1073/pnas.74.11.5088
470:10.1023/A:1004257523100
336:Molecular phylogenetics
186:to acquire one or more
20:Microbial phylogenetics
2294:Impedance microbiology
2035:Caenorhabditis elegans
1851:Microbial intelligence
1841:Microbial biogeography
395:Caister Academic Press
366:Caister Academic Press
2340:Microbial dark matter
2284:Dark-field microscopy
2088:Marine microorganisms
1964:Microbial cooperation
687:10.1073/pnas.74.2.560
389:Blum, P, ed. (2010).
172:enzyme RNA polymerase
1959:Microbial consortium
1856:Microbial metabolism
1512:Nature Biotechnology
1044:Bushman, F. (2002).
660:Maxam, A.M. (1977).
306:Comparative genomics
120:nucleotide sequences
32:comparative genomics
2062:Seagrass microbiome
1582:10.7554/eLife.21887
1280:Nature Microbiology
1142:2000Natur.405..299O
1081:(23): 10679–10684.
1017:(5423): 2124–2128.
918:1998PNAS...95.6578W
805:1990PNAS...87.4576W
678:1977PNAS...74..560M
619:1977PNAS...74.5463S
560:1977PNAS...74.5088W
40:comparative anatomy
2299:Microbial cytology
2263:Protein production
2098:Marine prokaryotes
1984:Microbial food web
1914:Protist locomotion
1892:Bacterial motility
1846:Microbial genetics
1641:10.7717/peerj.2969
1236:10.1101/gr.3666505
1179:Eisen, J. (2000).
513:10.1007/BF01058626
321:Bacterial taxonomy
61:genealogical trees
2403:
2402:
2174:Food microbiology
2067:Soil microbiology
2006:Microbial synergy
1974:Microbial ecology
1136:(6784): 299–304.
912:(12): 6578–6583.
854:(5313): 734–740.
799:(12): 4576–4579.
773:978-0-12-765560-4
613:(12): 5463–5467.
554:(11): 5088–5090.
404:978-1-904455-27-1
375:978-1-904455-67-7
174:). The resulting
2433:
2393:
2392:
2194:Human microbiome
2118:Coral microbiome
2052:Plant microbiome
1826:
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2103:Marine protists
2076:
2057:Root microbiome
2040:
1949:Biological pump
1930:
1880:
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1818:
1760:
1755:
1725:
1724:
1679:
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1499:
1458:(8): e1006242.
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1224:Genome Research
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1177:
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1038:
1007:
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980:10.1038/nrg1603
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2335:Deep biosphere
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2330:Bioremediation
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2289:DNA sequencing
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2093:Marine viruses
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2028:Quorum sensing
2025:
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2018:
2008:
2003:
1998:
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1996:
1991:
1989:microbial loop
1981:
1979:Microbial cyst
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1897:run-and-tumble
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1817:
1816:
1811:
1806:
1801:
1796:
1791:
1786:
1781:
1776:
1770:
1768:
1762:
1761:
1758:Microorganisms
1754:
1753:
1746:
1739:
1731:
1723:
1722:
1673:
1614:
1555:
1518:(9): 814–821.
1497:
1438:
1409:10.1086/417338
1403:(4): 411–453.
1383:
1338:Genome Biology
1321:
1286:(6): 652–661.
1259:
1230:(7): 954–959.
1210:
1191:(6): 606–611.
1171:
1120:
1061:
1054:
1036:
1001:
974:(5): 361–375.
951:
892:
873:
838:
779:
772:
754:
711:
672:(2): 560–564.
652:
593:
534:
491:
448:
429:(4): 780–795.
410:
403:
381:
374:
351:
350:
348:
345:
344:
343:
338:
333:
328:
323:
318:
313:
308:
301:
298:
292:
289:
283:
280:
271:
268:
259:
256:
227:
224:
206:
203:
163:
160:
107:
104:
100:Archaebacteria
52:
49:
47:
44:
24:microorganisms
16:Field of study
15:
9:
6:
4:
3:
2:
2438:
2427:
2424:
2422:
2419:
2417:
2416:Phylogenetics
2414:
2413:
2411:
2396:
2388:
2387:
2384:
2378:
2375:
2373:
2370:
2368:
2365:
2363:
2360:
2358:
2355:
2351:
2348:
2347:
2346:
2343:
2341:
2338:
2336:
2333:
2331:
2328:
2327:
2325:
2321:
2315:
2312:
2310:
2307:
2305:
2302:
2300:
2297:
2295:
2292:
2290:
2287:
2285:
2282:
2281:
2279:
2275:
2269:
2266:
2264:
2261:
2259:
2256:
2252:
2249:
2247:
2244:
2240:
2237:
2236:
2235:
2232:
2230:
2227:
2225:
2222:
2220:
2217:
2215:
2212:
2210:
2207:
2205:
2202:
2200:
2197:
2196:
2195:
2192:
2190:
2187:
2185:
2182:
2180:
2179:Microbial oil
2177:
2175:
2172:
2170:
2167:
2165:
2162:
2161:
2159:
2157:Human related
2155:
2149:
2146:
2144:
2143:Picoeukaryote
2141:
2139:
2136:
2134:
2131:
2129:
2126:
2124:
2121:
2119:
2116:
2114:
2111:
2109:
2106:
2104:
2101:
2099:
2096:
2094:
2091:
2089:
2086:
2085:
2083:
2079:
2073:
2070:
2068:
2065:
2063:
2060:
2058:
2055:
2053:
2050:
2049:
2047:
2043:
2037:
2036:
2031:
2029:
2026:
2022:
2019:
2017:
2014:
2013:
2012:
2009:
2007:
2004:
2002:
2001:Microbial mat
1999:
1995:
1992:
1990:
1987:
1986:
1985:
1982:
1980:
1977:
1975:
1972:
1970:
1967:
1965:
1962:
1960:
1957:
1955:
1952:
1950:
1947:
1945:
1942:
1941:
1939:
1937:
1933:
1927:
1924:
1920:
1917:
1916:
1915:
1912:
1908:
1905:
1903:
1900:
1898:
1895:
1894:
1893:
1890:
1889:
1887:
1883:
1877:
1874:
1872:
1869:
1867:
1864:
1862:
1859:
1857:
1854:
1852:
1849:
1847:
1844:
1842:
1839:
1838:
1836:
1834:
1830:
1825:
1815:
1812:
1810:
1807:
1805:
1802:
1800:
1797:
1795:
1794:Nanobacterium
1792:
1790:
1787:
1785:
1784:Cyanobacteria
1782:
1780:
1777:
1775:
1772:
1771:
1769:
1767:
1763:
1759:
1752:
1747:
1745:
1740:
1738:
1733:
1732:
1729:
1718:
1714:
1710:
1706:
1701:
1696:
1692:
1688:
1684:
1677:
1669:
1665:
1660:
1655:
1651:
1647:
1642:
1637:
1633:
1629:
1625:
1618:
1610:
1606:
1601:
1596:
1592:
1588:
1583:
1578:
1574:
1570:
1566:
1559:
1551:
1547:
1542:
1537:
1533:
1529:
1525:
1521:
1517:
1513:
1509:
1501:
1493:
1489:
1484:
1479:
1475:
1471:
1466:
1461:
1457:
1453:
1449:
1442:
1434:
1430:
1426:
1422:
1418:
1414:
1410:
1406:
1402:
1398:
1394:
1387:
1379:
1375:
1370:
1365:
1361:
1357:
1352:
1347:
1343:
1339:
1335:
1328:
1326:
1317:
1313:
1309:
1305:
1301:
1297:
1293:
1289:
1285:
1281:
1277:
1270:
1268:
1266:
1264:
1255:
1251:
1246:
1241:
1237:
1233:
1229:
1225:
1221:
1214:
1206:
1202:
1198:
1194:
1190:
1186:
1182:
1175:
1167:
1163:
1159:
1155:
1151:
1147:
1143:
1139:
1135:
1131:
1124:
1116:
1112:
1107:
1102:
1098:
1094:
1089:
1084:
1080:
1076:
1072:
1065:
1057:
1051:
1047:
1040:
1032:
1028:
1024:
1020:
1016:
1012:
1005:
997:
993:
989:
985:
981:
977:
973:
969:
962:
955:
947:
943:
938:
933:
928:
923:
919:
915:
911:
907:
903:
896:
888:
884:
877:
869:
865:
861:
857:
853:
849:
842:
834:
830:
825:
820:
815:
810:
806:
802:
798:
794:
790:
783:
775:
769:
765:
758:
750:
746:
742:
738:
734:
730:
726:
722:
715:
707:
703:
698:
693:
688:
683:
679:
675:
671:
667:
663:
656:
648:
644:
639:
634:
629:
624:
620:
616:
612:
608:
604:
597:
589:
585:
580:
575:
570:
565:
561:
557:
553:
549:
545:
538:
530:
526:
522:
518:
514:
510:
506:
502:
495:
487:
483:
479:
475:
471:
467:
464:(1): 85–111.
463:
459:
452:
444:
440:
436:
432:
428:
424:
417:
415:
406:
400:
396:
392:
385:
377:
371:
367:
363:
356:
352:
342:
341:Phylogenetics
339:
337:
334:
332:
329:
327:
324:
322:
319:
317:
314:
312:
311:Phylogenomics
309:
307:
304:
303:
297:
288:
279:
277:
267:
265:
255:
252:
248:
247:
243:
242:Small subunit
237:
233:
223:
220:
216:
212:
202:
200:
195:
193:
189:
185:
181:
177:
173:
169:
159:
155:
153:
149:
144:
142:
138:
134:
130:
125:
121:
117:
113:
103:
101:
97:
93:
92:ribosomal RNA
89:
86:, looking at
85:
81:
76:
74:
70:
66:
62:
58:
57:phylogenetics
43:
41:
37:
33:
29:
25:
21:
2345:Microswimmer
2239:in pregnancy
2189:Nylon-eating
2072:Spermosphere
2034:
1860:
1833:Microbiology
1690:
1686:
1676:
1631:
1627:
1617:
1572:
1568:
1558:
1515:
1511:
1500:
1455:
1451:
1441:
1400:
1396:
1386:
1344:(10): R151.
1341:
1337:
1283:
1279:
1227:
1223:
1213:
1188:
1184:
1174:
1133:
1129:
1123:
1078:
1074:
1064:
1045:
1039:
1014:
1010:
1004:
971:
967:
954:
909:
905:
895:
886:
882:
876:
851:
847:
841:
796:
792:
782:
763:
757:
724:
720:
714:
669:
665:
655:
610:
606:
596:
551:
547:
537:
507:(1): 21–59.
504:
500:
494:
461:
457:
451:
426:
422:
390:
384:
361:
355:
294:
285:
273:
261:
250:
245:
241:
229:
208:
196:
165:
156:
145:
109:
77:
54:
19:
18:
2377:Siderophore
2138:Phycosphere
1994:viral shunt
727:: 263–273.
176:genealogies
106:1980s–1990s
73:nucleotides
65:amino acids
51:1960s–1970s
2410:Categories
2277:Techniques
2108:Microalgae
2016:microbiota
2011:Microbiome
1799:Prokaryote
1055:0879696036
347:References
291:Challenges
217:plays for
154:on earth.
112:sequencing
80:Carl Woese
55:Microbial
36:physiology
2350:biohybrid
2204:dysbiosis
2021:holobiont
1919:amoeboids
1902:twitching
1709:0036-8075
1650:2167-8359
1634:: e2969.
1591:2050-084X
1532:1087-0156
1474:1553-7358
1417:0033-5770
1360:1465-6906
1300:2058-5276
1097:0027-8424
236:phylogeny
184:bacterium
135:of life:
122:of whole
28:evolution
2395:Category
2314:Staining
2246:placenta
1876:Virology
1871:Mycology
1809:Protozoa
1779:Bacteria
1717:26542581
1693:(6261).
1668:28289558
1609:28198697
1550:23975157
1492:30091981
1433:32027097
1378:18851752
1316:43962376
1308:29795540
1254:15965028
1205:11088009
1166:85739173
1158:10830951
1115:20495090
1031:10381871
996:16379422
988:15861208
749:26180176
521:11639258
486:29935487
478:11619919
443:18053933
300:See also
232:taxonomy
219:microbes
199:bacteria
137:Bacteria
114:RNA and
84:Bacteria
69:proteins
1944:Biofilm
1936:Ecology
1907:gliding
1804:Protist
1774:Archaea
1687:Science
1659:5345826
1600:5328592
1541:3819121
1483:6084841
1425:1784710
1369:2760878
1245:1172039
1138:Bibcode
1106:2890805
1011:Science
946:9618454
914:Bibcode
889:: 4–12.
868:9115194
848:Science
833:2112744
801:Bibcode
741:3472723
674:Bibcode
615:Bibcode
556:Bibcode
276:PICRUSt
152:biomass
141:Archaea
133:domains
46:History
2251:uterus
2234:vagina
2199:asthma
2081:Marine
2045:Plants
1885:Motion
1766:Groups
1715:
1707:
1666:
1656:
1648:
1607:
1597:
1589:
1548:
1538:
1530:
1490:
1480:
1472:
1431:
1423:
1415:
1376:
1366:
1358:
1314:
1306:
1298:
1252:
1242:
1203:
1164:
1156:
1130:Nature
1113:
1103:
1095:
1052:
1029:
994:
986:
944:
934:
866:
831:
821:
770:
747:
739:
706:265521
704:
697:392330
694:
647:271968
645:
638:431765
635:
588:270744
586:
579:432104
576:
529:367102
527:
519:
484:
476:
441:
401:
372:
244:(SSU)
211:Darwin
209:Since
2367:Omics
2323:Other
2224:mouth
2209:fecal
1814:Virus
1789:Fungi
1628:PeerJ
1569:eLife
1429:S2CID
1312:S2CID
1162:S2CID
992:S2CID
964:(PDF)
937:33863
824:54159
745:S2CID
525:S2CID
482:S2CID
192:genes
188:genes
162:2000s
124:genes
96:Woese
34:, as
2229:skin
2219:lung
1713:PMID
1705:ISSN
1664:PMID
1646:ISSN
1605:PMID
1587:ISSN
1546:PMID
1528:ISSN
1488:PMID
1470:ISSN
1421:PMID
1413:ISSN
1374:PMID
1356:ISSN
1304:PMID
1296:ISSN
1250:PMID
1201:PMID
1154:PMID
1111:PMID
1093:ISSN
1050:ISBN
1027:PMID
984:PMID
942:PMID
864:PMID
829:PMID
768:ISBN
737:PMID
702:PMID
643:PMID
584:PMID
517:PMID
474:PMID
439:PMID
399:ISBN
370:ISBN
264:PCMs
246:rRNA
234:and
168:rRNA
148:rRNA
71:and
38:and
2214:gut
1695:doi
1691:350
1654:PMC
1636:doi
1595:PMC
1577:doi
1536:PMC
1520:doi
1478:PMC
1460:doi
1405:doi
1364:PMC
1346:doi
1288:doi
1240:PMC
1232:doi
1193:doi
1146:doi
1134:405
1101:PMC
1083:doi
1079:107
1019:doi
1015:284
976:doi
932:PMC
922:doi
856:doi
852:276
819:PMC
809:doi
729:doi
692:PMC
682:doi
633:PMC
623:doi
574:PMC
564:doi
509:doi
466:doi
431:doi
215:HGT
116:DNA
88:RNA
67:of
2412::
1711:.
1703:.
1689:.
1685:.
1662:.
1652:.
1644:.
1630:.
1626:.
1603:.
1593:.
1585:.
1575:.
1571:.
1567:.
1544:.
1534:.
1526:.
1516:31
1514:.
1510:.
1486:.
1476:.
1468:.
1456:14
1454:.
1450:.
1427:.
1419:.
1411:.
1401:66
1399:.
1395:.
1372:.
1362:.
1354:.
1340:.
1336:.
1324:^
1310:.
1302:.
1294:.
1282:.
1278:.
1262:^
1248:.
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1228:15
1226:.
1222:.
1199:.
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1160:.
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904:.
887:51
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850:.
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611:74
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552:75
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425:.
413:^
397:.
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433::
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378:.
251:.
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