Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

28018325

DOI Digital object identifier for electronic documents.

10.3389/fmicb.2016.01997

URI

Authors

Nagpal R, Tsuji H, Takahashi T, Kawashima K, Nagata S, Nomoto K, Yamashiro Y

Journal

Frontiers in microbiology

Year

2016

Keywords:

C-section, Lactobacillus, RT-qPCR, dysbiosis, gut bacteria, intestinal microbiota, meconium

For decades, babies were thought to be born germ-free, but recent evidences suggest that they are already exposed to various bacteria in utero. However, the data on population levels of such pioneer gut bacteria, particularly in context to birth mode, is sparse. We herein aimed to quantify such bacteria from the meconium of 151 healthy term Japanese infants born vaginally or by C-section. Neonatal first meconium was obtained within 24-48 h of delivery; RNA was extracted and subjected to reverse-transcription-quantitative PCR using specific primers for Clostridium coccoides group, C. leptum subgroup, Bacteroides fragilis group, Atopobium cluster, Prevotella, Bifidobacterium, Lactobacillus, Enterococcus, Enterobacteriaceae, Staphylococcus, Enterococcus, Streptococcus, C. perfringens, and C. difficile. We detected several bacterial groups in both vaginally- and cesarean-born infants. B. fragilis group, Enterobacteriaceae, Enterococcus, Streptococcus, and Staphylococcus were detected in more than 50% of infants, with counts ranging from 105 to 108 cells/g sample. About 30-35% samples harbored Bifidobacterium and Lactobacillus (104-105 cells/g); whereas C. coccoides group, C. leptum subgroup and C. perfringens were detected in 10-20% infants (103-105 cells/g). Compared to vaginally-born babies, cesarean-born babies were significantly less often colonized with Lactobacillus genus (6% vs. 37%; P = 0.01) and Lactobacillus gasseri subgroup (6% vs. 31%; P = 0.04). Overall, seven Lactobacillus subgroups/species, i.e., L. gasseri subgroup, L. ruminis subgroup, L. casei subgroup, L. reuteri subgroup, L. sakei subgroup, L. plantarum subgroup, and L. brevis were detected in the samples from vaginally-born group, whereas only two members, i.e., L. gasseri subgroup and L. brevis were detected in the cesarean group. These data corroborate that several bacterial clades may already be present before birth in term infants' gut. Further, lower detection rate of lactobacilli in cesarean-born babies suggests that the primary source of lactobacilli in infant gut is mainly from maternal vaginal and-to a lesser extent-anal microbiota during vaginal delivery, and that the colonization by some important Lactobacillus species is delayed in babies delivered via cesarean-section.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Chloe

Subjects

Location of subjects: Japan

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Cesarean section caesarean section,Cesarean section,cesarean section

Group 0 name Corresponds to the control (unexposed) group for case-control studies: vaginal delivery after 7 days of delivery

Group 1 name Corresponds to the case (exposed) group for case-control studies: C-section delivery

Group 0 sample size Number of subjects in the control (unexposed) group: 134

Group 1 sample size Number of subjects in the case (exposed) group: 17

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): No information about pre-delivey duration. 3 Vaginally-delivered infants have been exposed to antibiotics (birth to sampling)

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: RT-qPCR

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: T-Test

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 2

Description: Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.

Abundance in Group 1: decreased abundance in C-section delivery

NCBI	Quality Control	Links
Lactobacillus gasseri

Revision editor(s): WikiWorks

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: vaginal delivery after 3 months of delivery

Lab analysis

Statistical Analysis

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 2

Description: Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.

Abundance in Group 1: decreased abundance in C-section delivery

NCBI	Quality Control	Links
Lactobacillus

Revision editor(s): WikiWorks

Experiment 3

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: vaginal delivery after 6 months of delivery

Lab analysis

Statistical Analysis

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 2

Description: Differences in the detection rate of Lactobacillus genus, subgroups and species between vaginally- and cesarean-born babies at different time-points during the first 3 years of life.

Abundance in Group 1: decreased abundance in C-section delivery

NCBI	Quality Control	Links
Limosilactobacillus reuteri

Revision editor(s): WikiWorks