Bacterial DNA is present in the fetal intestine and overlaps with that in the placenta in mice

PLoS ONE

Volumn 13, Issue 5, 2018, Pages

  Martinez, Keith A ^a,b   Romano Keeler, Joann ^c,g   Zackular, Joseph P ^d   Moore, Daniel J ^c,d   Brucker, Robert M ^e,h   Hooper, Christopher ^c   Meng, Shufang ^c   Brown, Naoko ^c   Mallal, Simon ^c,d,f   Reese, Jeff ^c,d   Aronoff, David M ^c,d   Shin, Hakdong ^b,i   Dominguez Bello, Maria Gloria ^a,j   Weitkamp, Jörn Hendrik ^c  

^a Sackler Institute   (United States)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^d VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e VANDERBILT UNIVERSITY   (United States)

^f MURDOCH UNIVERSITY   (Australia)

^g Mednax Corporation   (United States)

^h HARVARD UNIVERSITY   (United States)

ⁱ Sejong University   (South Korea)

^j RUTGERS UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

ARTICLE; BACTERIAL GENE; BURKHOLDERIACEAE; COLON; CONTROLLED STUDY; ENTEROCOCCUS; FECES; FETUS; GENETIC VARIABILITY; GESTATIONAL AGE; INTESTINE; LACHNOSPIRACEAE; MOTHER; MOUSE; MOUTH; NEWBORN; NONHUMAN; PHYLOGENY; PHYLUM; PLACENTA; POLYMERASE CHAIN REACTION; STAPHYLOCOCCUS; STREPTOCOCCUS; VAGINA; AMNION FLUID; ANIMAL; EMBRYOLOGY; FEMALE; GENETICS; METABOLISM; MICROBIOLOGY; PREGNANCY;

AMNIOTIC FLUID; ANIMALS; DNA, BACTERIAL; FEMALE; INTESTINES; MICE; PLACENTA; PREGNANCY; RNA, RIBOSOMAL, 16S; VAGINA;

EID: 85047312736     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0197439     Document Type: Article

References (34)

1. Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, et al. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One 2014; 9: e90784, https://doi.org/10.1371/journal.pone.0090784 PMID: 24614698
2. DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, et al. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS One 2008; 3: e3056, https://doi.org/10.1371/journal.pone.0003056 PMID: 18725970
3. Han YW, Shen T, Chung P, Buhimschi IA, Buhimschi CS. Uncultivated bacteria as etiologic agents of intra-amniotic inflammation leading to preterm birth. J Clin Microbiol 2009; 47: 38–47, https://doi.org/10.1128/JCM.01206-08 PMID: 18971361
4. Chernikova DA, Koestler DC, Hoen AG, Housman ML, Hibberd PL, Moore JH, et al. Fetal exposures and perinatal influences on the stool microbiota of premature infants. J Matern Fetal Neonatal Med 2016; 29: 99–105, https://doi.org/10.3109/14767058.2014.987748 PMID: 25394613
5. Funkhouser LJ, Bordenstein SR. Mom knows best: the universality of maternal microbial transmission. PLoS Biol 2013; 11: e1001631, https://doi.org/10.1371/journal.pbio.1001631 PMID: 23976878
6. Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, et al. Is meconium from healthy newborns actually sterile? Res Microbiol 2008; 159: 187–193, https://doi.org/10.1016/j.resmic.2007.12.007PMID: 18281199
7. Jiménez E, Fernández L, Marín ML, Martín R, Odriozola JM, Nueno-Palop C, et al. Isolation of com-mensal bacteria from umbilical cord blood of healthy neonates born by cesarean section. Curr Microbiol 2005; 51: 270–274, https://doi.org/10.1007/s00284-005-0020-3 PMID: 16187156
8. Zheng J, Xiao X, Zhang Q, Mao L, Yu M, Xu J, et al. The Placental Microbiome Varies in Association with Low Birth Weight in Full-Term Neonates. Nutrients 2015; 7: 6924–6937, https://doi.org/10.3390/ nu7085315 PMID: 26287241
9. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J, et al. The placenta harbors a unique microbiome. Sci Transl Med 2014, 6, 237ra265, https://doi.org/10.1126/scitranslmed.3008599 PMID: 24848255
10. Collado MC, Rautava S, Aakko J, Isolauri E, Salminen, S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep 2016; 6: 23129, https://doi.org/10.1038/srep23129 PMID: 27001291
11. Amarasekara R, Jayasekara RW, Senanayake H, Dissanayake VH. Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia. J Obstet Gynaecol Res 2015, 41, 662–669, https://doi.org/10.1111/jog.12619 PMID: 25492799
12. Antony KM, Ma J, Mitchell KB, Racusin DA, Versalovic J, Aagaard K et al. The preterm placental microbiome varies in association with excess maternal gestational weight gain. Am J Obstet Gynecol 2015; 212: 653 e651-616, https://doi.org/10.1016/j.ajog.2014.12.041 PMID: 25557210
13. Prince AL, Ma J, Kannan PS, Alvarez M, Gisslen T, Harris RA, et al. The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis. Am J Obstet Gynecol 2016; 214: 627 e621-627 e616, https://doi.org/10.1016/j.ajog.2016.01.193 PMID: 26965447
14. Romano-Keeler J, Moore DJ, Wang C, Brucker RM, Fonnesbeck C, Slaughter JC, et al. Early life establishment of site-specific microbial communities in the gut. Gut Microbes 2014; 5: 192–201, https://doi.org/10.4161/gmic.28442 PMID: 24637795
15. Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M, et al. The early infant gut microbiome varies in association with a maternal high-fat diet. Genome Med 2016; 8: 77, https://doi.org/10.1186/ s13073-016-0330-z PMID: 27503374
16. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014; 12: 87, https://doi.org/10.1186/s12915-014-0087-z PMID: 25387460
17. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73: 5261–5267, https://doi.org/10.1128/AEM.00062-07 PMID: 17586664
18. Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R et al. Biphasic assembly of the murine intestinal microbiota during early development. ISME J 2013; 7: 1112–1115, https://doi.org/10.1038/ismej.2013.15 PMID: 23535917
19. Zheng W, Tsompana M, Ruscitto A, Sharma A, Genco R, Sun Y, et al. An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome 2015; 3: 48, https://doi.org/10.1186/s40168-015-0110-9 PMID: 26437933
20. Pammi M, O’Brien JL, Ajami NJ, Wong MC, Versalovic J, Petrosino JF. Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study. PLoS One 2017; 12: e0176669, https://doi.org/10.1371/journal.pone.0176669 PMID: 28448623
21. Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med 2017; 23: 314–326, https://doi.org/10.1038/nm.4272 PMID: 28112736
22. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006; 118: 511–521, https://doi.org/10.1542/peds.2005-2824 PMID: 16882802
23. Kriegel MA, Sefik E, Hill JA, Wu HJ, Benoist C, Mathis D. Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice. Proc Natl Acad Sci U S A 2011; 108: 11548–11553, https://doi.org/10.1073/pnas.1108924108 PMID: 21709219
24. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010; 107: 11971–11975, https://doi.org/10.1073/pnas.1002601107 PMID: 20566857
25. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013; 79: 5112–5120, https://doi.org/10.1128/AEM.01043-13PMID: 23793624
26. Junicke H, Abbas B, Oentoro J, van Loosdrecht M, Kleerebezem R. Absolute quantification of individual biomass concentrations in a methanogenic coculture. AMB Express 2014; 4: 35, https://doi.org/10.1186/s13568-014-0035-x PMID: 24949269
27. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75: 7537–7541, AEM.01541-09 [pii] https://doi.org/10.1128/AEM.01541-09 PMID: 19801464
28. Zackular J P, Rogers MA, Ruffin MT, Schloss PD. The human gut microbiome as a screening tool for colorectal cancer. Cancer Prev Res 2014; 7: 1112–1121, https://doi.org/10.1158/1940-6207.CAPR-14-0129 PMID: 25104642
29. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7: 335–336, https://doi.org/10.1038/nmeth.f.303 PMID: 20383131
30. Edgar RC, Haas BJ, Clemente J C, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011; 27: 2194–2200, https://doi.org/10.1093/bioinformatics/btr381PMID: 21700674
31. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J 2011; 5: 169–172, https://doi.org/10.1038/ismej.2010.133PMID: 20827291
32. Bray JR, Curtis JT. An ordination of the upland forest communities of southern Wisconsin. Ecol Monogr 1957; 2:, 326–349.
33. Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecology 2001; 26: 32–46, https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x
34. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12: R60, https://doi.org/10.1186/gb-2011-12-6-r60 PMID: 21702898