|
1
|
Zilberman-Schapira G, Zmora N, Itav S,
Bashiardes S, Elinav H and Elinav E: The gut microbiome in human
immunodeficiency virus infection. BMC Med. 14(83)2016.PubMed/NCBI View Article : Google Scholar
|
|
2
|
Cohen CR, Lingappa JR, Baeten JM, Ngayo
MO, Spiegel CA, Hong T, Donnell D, Celum C, Kapiga S, Delany S, et
al: Bacterial vaginosis associated with increased risk of
female-to-male HIV-1 transmission: A prospective cohort analysis
among African couples. PLoS Med. 9(e1001251)2012.PubMed/NCBI View Article : Google Scholar
|
|
3
|
Dillon SM, Lee EJ, Kotter CV, Austin GL,
Dong Z, Hecht DK, Gianella S, Siewe B, Smith DM, Landay AL, et al:
An altered intestinal mucosal microbiome in HIV-1 infection is
associated with mucosal and systemic immune activation and
endotoxemia. Mucosal Immunol. 7:983–994. 2014.PubMed/NCBI View Article : Google Scholar
|
|
4
|
Doerflinger SY, Throop AL and
Herbst-Kralovetz MM: 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.
209:1989–1999. 2014.PubMed/NCBI View Article : Google Scholar
|
|
5
|
Gori A, Tincati C, Rizzardini G, Torti C,
Quirino T, Haarman M, Ben Amor K, van Schaik J, Vriesema A, Knol J,
et al: Early impairment of gut function and gut flora supporting a
role for alteration of gastrointestinal mucosa in human
immunodeficiency virus pathogenesis. J Clin Microbiol. 46:757–758.
2008.PubMed/NCBI View Article : Google Scholar
|
|
6
|
Brenchley JM, Price DA, Schacker TW, Asher
TE, Silvestri G, Rao S, Kazzaz Z, Bornstein E, Lambotte O, Altmann
D, et al: Microbial translocation is a cause of systemic immune
activation in chronic HIV infection. Nat Med. 12:1365–1371.
2006.PubMed/NCBI View
Article : Google Scholar
|
|
7
|
Blumberg R and Powrie F: Microbiota,
disease, and back to health: A metastable journey. Sci Transl Med.
4(137rv7)2012.PubMed/NCBI View Article : Google Scholar
|
|
8
|
Zoetendal EG, von Wright A,
Vilpponen-Salmela T, Ben-Amor K, Akkermans AD and de Vos WM:
Mucosa-associated bacteria in the human gastrointestinal tract are
uniformly distributed along the colon and differ from the community
recovered from feces. Appl Environ Microbiol. 68:3401–3407.
2002.PubMed/NCBI View Article : Google Scholar
|
|
9
|
Durbán A, Abellán JJ, Jiménez-Hernández N,
Salgado P, Ponce M, Ponce J, Garrigues V, Latorre A and Moya A:
Structural alterations of faecal and mucosa-associated bacterial
communities in irritable bowel syndrome. Environ Microbiol Rep.
4:242–247. 2012.PubMed/NCBI View Article : Google Scholar
|
|
10
|
Ringel Y, Maharshak N, Ringel-Kulka T,
Wolber EA, Sartor RB and Carroll IM: High throughput sequencing
reveals distinct microbial populations within the mucosal and
luminal niches in healthy individuals. Gut Microbes. 6:173–181.
2015.PubMed/NCBI View Article : Google Scholar
|
|
11
|
Tap J, Derrien M, Törnblom H, Brazeilles
R, Cools-Portier S, Doré J, Störsrud S, Le Nevé B, Öhman L and
Simrén M: Identification of an intestinal microbiota signature
associated with severity of irritable bowel syndrome.
Gastroenterology. 152:111–123.e8. 2017.PubMed/NCBI View Article : Google Scholar
|
|
12
|
Zhang L, Chow EP, Jing J, Zhuang X, Li X,
He M, Sun H, Li X, Gorgens M, Wilson D, et al: HIV prevalence in
China: Integration of surveillance data and a systematic review.
Lancet Infect Dis. 13:955–963. 2013.PubMed/NCBI View Article : Google Scholar
|
|
13
|
Ling Z, Jin C, Xie T, Cheng Y, Li L and Wu
N: Alterations in the fecal microbiota of patients with HIV-1
infection: An Observational Study in A Chinese Population. Sci Rep.
6(30673)2016.PubMed/NCBI View Article : Google Scholar
|
|
14
|
Sun Y, Ma Y, Lin P, Tang YW, Yang L, Shen
Y, Zhang R, Liu L, Cheng J, Shao J, et al: Fecal bacterial
microbiome diversity in chronic HIV-infected patients in China.
Emerg Microbes Infect. 5(e31)2016.PubMed/NCBI View Article : Google Scholar
|
|
15
|
Zhou Y, Ou Z, Tang X, Zhou Y, Xu H, Wang
X, Li K, He J, Du Y, Wang H, et al: Alterations in the gut
microbiota of patients with acquired immune deficiency syndrome. J
Cell Mol Med. 22:2263–2271. 2018.PubMed/NCBI View Article : Google Scholar
|
|
16
|
Lozupone CA, Li M, Campbell TB, Flores SC,
Linderman D, Gebert MJ, Knight R, Fontenot AP and Palmer BE:
Alterations in the gut microbiota associated with HIV-1 infection.
Cell Host Microbe. 14:329–339. 2013.PubMed/NCBI View Article : Google Scholar
|
|
17
|
Caporaso JG, Kuczynski J, Stombaugh J,
Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich
JK, Gordon JI, et al: QIIME allows analysis of high-throughput
community sequencing data. Nat Methods. 7:335–336. 2010.PubMed/NCBI View Article : Google Scholar
|
|
18
|
Kuczynski J, Stombaugh J, Walters WA,
Gonzalez A, Caporaso JG and Knight R: Using QIIME to analyze 16S
rRNA gene sequences from microbial communities. Curr Protoc
Bioinformatics. Chapter 10: Unit 10.7:2011.PubMed/NCBI View Article : Google Scholar
|
|
19
|
Wang Q, Garrity GM, Tiedje JM and Cole JR:
Naive Bayesian classifier for rapid assignment of rRNA sequences
into the new bacterial taxonomy. Appl Environ Microbiol.
73:5261–5267. 2007.PubMed/NCBI View Article : Google Scholar
|
|
20
|
Li B, Zhang X, Guo F, Wu W and Zhang T:
Characterization of tetracycline resistant bacterial community in
saline activated sludge using batch stress incubation with
high-throughput sequencing analysis. Water Res. 47:4207–4216.
2013.PubMed/NCBI View Article : Google Scholar
|
|
21
|
Lozupone C and Knight R: UniFrac: A new
phylogenetic method for comparing microbial communities. Appl
Environ Microbiol. 71:8228–8235. 2005.PubMed/NCBI View Article : Google Scholar
|
|
22
|
Nagpal R, Shively CA, Appt SA, Register
TC, Michalson KT, Vitolins MZ and Yadav H: Gut Microbiome
Composition in Non-human Primates Consuming a Western or
Mediterranean Diet. Front Nutr. 5(28)2018.PubMed/NCBI View Article : Google Scholar
|
|
23
|
Segata N, Izard J, Waldron L, Gevers D,
Miropolsky L, Garrett WS and Huttenhower C: Metagenomic biomarker
discovery and explanation. Genome Biol. 12(R60)2011.PubMed/NCBI View Article : Google Scholar
|
|
24
|
Lo Presti A, Zorzi F, Del Chierico F,
Altomare A, Cocca S, Avola A, De Biasio F, Russo A, Cella E, Reddel
S, et al: Fecal and mucosal microbiota profiling in irritable bowel
syndrome and inflammatory bowel disease. Front Microbiol.
10(1655)2019.PubMed/NCBI View Article : Google Scholar
|
|
25
|
Mira-Pascual L, Cabrera-Rubio R, Ocon S,
Costales P, Parra A, Suarez A, Moris F, Rodrigo L, Mira A and
Collado MC: Microbial mucosal colonic shifts associated with the
development of colorectal cancer reveal the presence of different
bacterial and archaeal biomarkers. J Gastroenterol. 50:167–179.
2015.PubMed/NCBI View Article : Google Scholar
|
|
26
|
Dinh DM, Volpe GE, Duffalo C, Bhalchandra
S, Tai AK, Kane AV, Wanke CA and Ward HD: Intestinal microbiota,
microbial translocation, and systemic inflammation in chronic HIV
infection. J Infect Dis. 211:19–27. 2015.PubMed/NCBI View Article : Google Scholar
|
|
27
|
Gasperotti AF, Revuelta MV, Studdert CA
and Herrera-Seitz MK: Identification of two different chemosensory
pathways in representatives of the genus Halomonas. BMC Genomics.
19(266)2018.PubMed/NCBI View Article : Google Scholar
|
|
28
|
Janda JM and Abbott SL: The genus
Shewanella: From the briny depths below to human pathogen. Crit Rev
Microbiol. 40:293–312. 2014.PubMed/NCBI View Article : Google Scholar
|
|
29
|
Long MR, Zhang DF, Yang XY, Zhang XM,
Zhang YG, Zhang YM, Zhu H and Li WJ: Halomonas nanhaiensis sp.
nov., a halophilic bacterium isolated from a sediment sample from
the South China Sea. Antonie van Leeuwenhoek. 103:997–1005.
2013.PubMed/NCBI View Article : Google Scholar
|
|
30
|
Noguera-Julian M, Rocafort M, Guillén Y,
Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M,
Bellido R, et al: Gut microbiota linked to sexual preference and
HIV infection. EBioMedicine. 5:135–146. 2016.PubMed/NCBI View Article : Google Scholar
|
|
31
|
Drago L, Toscano M, De Grandi R, Casini V
and Pace F: Persisting changes of intestinal microbiota after bowel
lavage and colonoscopy. Eur J Gastroenterol Hepatol. 28:532–537.
2016.PubMed/NCBI View Article : Google Scholar
|
|
32
|
Vich Vila A, Collij V, Sanna S, Sinha T,
Imhann F, Bourgonje AR, Mujagic Z, Jonkers DMAE, Masclee AAM, Fu J,
et al: Impact of commonly used drugs on the composition and
metabolic function of the gut microbiota. Nat Commun.
11(362)2020.PubMed/NCBI View Article : Google Scholar
|
|
33
|
Tropini C, Moss EL, Merrill BD, Ng KM,
Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM,
Elias JE, et al: Transient osmotic perturbation causes long-term
alteration to the gut microbiota. Cell. 173:1742–1754.e1717.
2018.PubMed/NCBI View Article : Google Scholar
|
|
34
|
Villanueva-Millán MJ, Pérez-Matute P,
Recio-Fernández E, Lezana Rosales JM and Oteo JA: Differential
effects of antiretrovirals on microbial translocation and gut
microbiota composition of HIV-infected patients. J Int AIDS Soc.
20(21526)2017.PubMed/NCBI View Article : Google Scholar
|
|
35
|
Nowak RG, Bentzen SM, Ravel J, Crowell TA,
Dauda W, Ma B, Liu H, Blattner WA, Baral SD and Charurat ME:
TRUSTRV368 Study Group: Rectal microbiota among HIV-uninfected,
untreated HIV, and treated HIV-infected in Nigeria. AIDS.
31:857–862. 2017.PubMed/NCBI View Article : Google Scholar
|
|
36
|
Ashuro AA, Lobie TA, Ye DQ, Leng RX, Li
BZ, Pan HF and Fan YG: Review on the alteration of gut microbiota:
The role of HIV infection and old age. AIDS Res Hum Retroviruses.
36:556–565. 2020.PubMed/NCBI View Article : Google Scholar
|
|
37
|
Bayigga L, Kateete DP, Anderson DJ,
Sekikubo M and Nakanjako D: Diversity of vaginal microbiota in
sub-Saharan Africa and its effects on HIV transmission and
prevention. Am J Obstet Gynecol. 220:155–166. 2019.PubMed/NCBI View Article : Google Scholar
|
|
38
|
Hager CL and Ghannoum MA: The mycobiome in
HIV. Curr Opin HIV AIDS. 13:69–72. 2018.PubMed/NCBI View Article : Google Scholar
|
|
39
|
Tuddenham S, Koay WL and Sears C: HIV,
sexual orientation, and gut microbiome interactions. Dig Dis Sci.
65:800–817. 2020.PubMed/NCBI View Article : Google Scholar
|
