Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-4-8
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Hanachi M, Maghrebi O, Bichiou H, Trabelsi F, Bouyahia NM, Zhioua F, Belghith M, Harigua-Souiai E, Baouendi M, Guizani-Tabbane L, Benkahla A, Souiai O
Journal
Frontiers in microbiology
Year
2022
Keywords:
ESKAPE bacteria, Tunisia, elective cesarean deliveries, microbiome, newborns, shotgun metagenome sequencing
Microbiota colonization is a dynamic process that impacts the health status during an individual's lifetime. The composition of the gut microbiota of newborns is conditioned by multiple factors, including the delivery mode (DM). Nonetheless, the DM's influence remains uncertain and is still the subject of debate. In this context, the medical indication and the emergency of a cesarean delivery might have led to confounding conclusions regarding the composition and diversity of the neonatal microbiome. Herein, we used high-resolution shotgun sequencing to decipher the composition and dynamics of the gut microbiota composition of Tunisian newborns. Stool samples were collected from 5 elective cesarean section (ECS) and 5 vaginally delivered (VD) newborns at the following time points: Day 0, Day 15, and Day 30. The ECS and VD newborns showed the same level of bacterial richness and diversity. In addition, our data pointed to a shift in microbiota community composition during the first 2 weeks, regardless of the DM. Both ECS and VD showed a profile dominated by Proteobacteria, Actinobacteria, and Firmicutes. However, ECS showed an underrepresentation of Bacteroides and an enrichment of opportunistic pathogenic species of the ESKAPE group, starting from the second week. Besides revealing the intestinal microbiota of Tunisian newborns, this study provides novel insights into the microbiota perturbations caused by ECS.

Experiment 1


Reviewed Marked as Reviewed by Folakunmi on 2024-4-8

Curated date: 2024/03/09

Curator: Ayibatari

Revision editor(s): Ayibatari

Subjects

Location of subjects
Tunisia
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
Delivery method DeliveryMethod,Delivery method,delivery method
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Vaginally Delivered(VD)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Elective Cesarean Section (ECS)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants whose delivery mode (DM) was through elective cesarean section (ECS)
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
5
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Last trimester of pregnancy.

Lab analysis

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

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-4-5

Curated date: 2024/03/11

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Supplementary Figure 2 c.

Description: Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.

Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS)

NCBI Quality ControlLinks
Actinomyces oris
Bifidobacterium dentium
Citrobacter braakii
Clostridiaceae
Clostridium
Clostridium perfringens
Stenotrophomonas maltophilia
Citrobacter freundii complex sp. CFNIH9
Enterobacter sp. E20
Actinomyces sp. oral taxon 414
Actinomyces sp. oral taxon 897

Revision editor(s): Ayibatari

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-4-5

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Supplementary Figure 2 c.

Description: Differentially abundant taxa between elective cesarean section (ECS) versus vaginally delivered (VD) newborns detected by linear discriminant analysis effect size (LEfSe) analysis.

Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS)

NCBI Quality ControlLinks
Alistipes shahii
Bacteroidales
Bacteroides helcogenes
Bacteroides heparinolyticus
Bacteroides ovatus
Bacteroidia
Bifidobacterium pseudocatenulatum
Dialister
Dialister massiliensis
Gardnerella
Gardnerella vaginalis
Parabacteroides
Parabacteroides distasonis

Revision editor(s): Ayibatari

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-4-8

Curated date: 2024/03/11

Curator: Ayibatari

Revision editor(s): Ayibatari

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Vaginally Delivered(VD) at Day 0
Group 1 name Corresponds to the case (exposed) group for case-control studies
Elective Cesarean Section (ECS) at Day 0

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-4-5

Curated date: 2024/03/11

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Figure 4 A.

Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.

Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS) at Day 0

NCBI Quality ControlLinks
Citrobacter
Citrobacter freundii
Clostridia
Eubacteriales

Revision editor(s): Ayibatari

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-4-5

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Figure 4 A.

Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 0 (A). Relative abundance of ESKAPE members in ECS newborns at each collection time point.

Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS) at Day 0

NCBI Quality ControlLinks
Methylorubrum
Methylorubrum populi

Revision editor(s): Ayibatari

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-4-8

Curated date: 2024/03/11

Curator: Ayibatari

Revision editor(s): Ayibatari

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Vaginally Delivered(VD) at Day 15
Group 1 name Corresponds to the case (exposed) group for case-control studies
Elective Cesarean Section (ECS) at Day 15

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-4-7

Curated date: 2024/03/11

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Figure 4 B.

Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.

Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS) at Day 15

NCBI Quality ControlLinks
Clostridiaceae
Clostridium
Bifidobacterium dentium
Actinomyces oris
Actinomyces sp. oral taxon 897
Bifidobacterium actinocoloniiforme

Revision editor(s): Ayibatari

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-4-7

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Figure 4 B.

Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 15 (B). Relative abundance of ESKAPE members in ECS newborns at each collection time point.

Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS) at Day 15

NCBI Quality ControlLinks
Enterobacterales
Enterobacteriaceae
Pseudomonadota
Gammaproteobacteria
Escherichia
Escherichia coli
Bacteroidia
Bacteroidales
Shigella
Bifidobacterium pseudocatenulatum
Bifidobacterium catenulatum subsp. kashiwanohense
Shigella dysenteriae
Bacteroides heparinolyticus
Citrobacter koseri
Megasphaera
Escherichia marmotae
Pectobacteriaceae

Revision editor(s): Ayibatari

Experiment 4


Reviewed Marked as Reviewed by Folakunmi on 2024-4-8

Curated date: 2024/03/11

Curator: Ayibatari

Revision editor(s): Ayibatari

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Vaginally Delivered(VD) at Day 30
Group 1 name Corresponds to the case (exposed) group for case-control studies
Elective Cesarean Section (ECS) at Day 30

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-4-7

Curated date: 2024/03/11

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Figure 4 C.

Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.

Abundance in Group 1: increased abundance in Elective Cesarean Section (ECS) at Day 30

NCBI Quality ControlLinks
Enterobacter cloacae
Klebsiella oxytoca
Enterobacter cloacae complex sp.
Enterobacter sp. Crenshaw
Klebsiella sp. M5al
Citrobacter braakii
Enterobacter bugandensis
Lelliottia nimipressuralis
Candidatus Hamiltonella
Candidatus Hamiltonella defensa
Lachnoanaerobaculum umeaense
Lachnoanaerobaculum
Bacillales

Revision editor(s): Ayibatari

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-4-7

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Figure 4 C.

Description: Differentially abundant taxa between ECS and VD newborns at each collection data. Linear discriminant analysis effect size (LEfSe) analysis of metagenomic sequences from ECS and VD newborn stool samples at Day 30 (C). Relative abundance of ESKAPE members in ECS newborns at each collection time point.

Abundance in Group 1: decreased abundance in Elective Cesarean Section (ECS) at Day 30

NCBI Quality ControlLinks
Bifidobacterium pseudocatenulatum
Bacteroides ovatus
Tannerellaceae
Parabacteroides
Parabacteroides distasonis
Flavobacteriales
Flavobacteriia
Flavobacteriaceae
Porphyromonadaceae
Corynebacterium diphtheriae
Synergistaceae
Synergistales
Synergistia
Synergistota
Dialister massiliensis
Gardnerella vaginalis
Gardnerella

Revision editor(s): Ayibatari

Experiment 5


Reviewed Marked as Reviewed by Svetlana up on 2024-4-11

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Not specified
Group 1 name Corresponds to the case (exposed) group for case-control studies
An experiment for group 1 (day 0) vs. group 0 (days 15 and 30)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Tunisian newborns' at day 0 sampling time points.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-4-11

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Supplementary Table_3.

Description: Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 0 with Day 15 and Day 30 .

Abundance in Group 1: increased abundance in An experiment for group 1 (day 0) vs. group 0 (days 15 and 30)

NCBI Quality ControlLinks
Comamonadaceae
Xanthomonadaceae
Xanthomonadales
Stenotrophomonas
Pseudomonadaceae
Pseudomonas
Methylorubrum

Revision editor(s): Ayibatari

Experiment 6


Reviewed Marked as Reviewed by Svetlana up on 2024-4-11

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
An experiment for group 1 (day 15) vs. group 0 (days 0 and 30)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Tunisian newborns' at day 15 sampling time points.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-4-11

Curated date: 2024/04/08

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Supplementary Table_3.

Description: Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 15 with Day 0 and Day 30 .

Abundance in Group 1: increased abundance in An experiment for group 1 (day 15) vs. group 0 (days 0 and 30)

NCBI Quality ControlLinks
Actinomycetota
Bifidobacteriales
Bifidobacteriaceae
Bifidobacterium
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria
Bifidobacterium breve
Klebsiella
Escherichia
Escherichia coli
Bifidobacterium longum
Bifidobacterium bifidum
Bacilli
Lactobacillaceae
Lactobacillales
Lactobacillus
Salmonella
Salmonella enterica
Bacillales
Staphylococcaceae
Staphylococcus
Klebsiella aerogenes
Negativicoccus massiliensis
Negativicoccus
Staphylococcus epidermidis
Shigella
Shigella flexneri
Limosilactobacillus fermentum
Staphylococcus hominis
Streptococcus pasteurianus
Bifidobacterium catenulatum subsp. kashiwanohense
Shigella dysenteriae
Bifidobacterium catenulatum
Acidaminococcus intestini
Corynebacteriaceae
Corynebacterium
Mycobacteriales
Enterobacter bugandensis
Streptococcus parasanguinis
Lactobacillus crispatus
Corynebacterium atypicum

Revision editor(s): Folakunmi

Experiment 7


Reviewed Marked as Reviewed by Svetlana up on 2024-4-11

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
An experiment for group 1 (day 30) vs. group 0 (days 0 and 15)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Tunisian newborns' at day 30 sampling time points.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-4-11

Curated date: 2024/03/17

Curator: Ayibatari

Revision editor(s): Ayibatari

Source: Supplementary Table_3.

Description: Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns at Day 30 with Day 0 and Day 15.

Abundance in Group 1: increased abundance in An experiment for group 1 (day 30) vs. group 0 (days 0 and 15)

NCBI Quality ControlLinks
Bacteroides thetaiotaomicron
Bifidobacterium adolescentis
Bifidobacterium pseudocatenulatum
Blautia
Blautia hansenii
Citrobacter
Citrobacter freundii
Clostridia
Clostridiaceae
Clostridium
Clostridium perfringens
Coriobacteriaceae
Coriobacteriales
Coriobacteriia
Cutibacterium avidum
Enterobacter
Enterobacter asburiae
Enterobacter cloacae
Enterobacter cloacae complex sp.
Enterobacter hormaechei
Enterobacter sp. Crenshaw
Enterococcaceae
Enterococcus
Enterococcus faecalis
Eubacteriaceae
Eubacterium
Eubacterium limosum
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Haemophilus
Klebsiella michiganensis
Klebsiella oxytoca
Klebsiella quasipneumoniae
Klebsiella variicola
Lachnoclostridium
Lachnospiraceae
Negativicutes
Pasteurellaceae
Pasteurellales
Pectobacteriaceae
Raoultella
Raoultella ornithinolytica
Serratia
Streptococcaceae
Streptococcus
Streptococcus equinus
Streptococcus gordonii
Streptococcus infantarius
Streptococcus mitis
Streptococcus salivarius
Streptococcus sp. FDAARGOS_192
Streptococcus thermophilus
Veillonella
Veillonella parvula
Veillonella rodentium
Veillonellaceae
Veillonellales
Yersiniaceae
Lachnospiraceae_Unmatched_GenusLachnospiraceae_Unmatched_Genus
Enterobacteriaceae_Unmatched_GenusEnterobacteriaceae_Unmatched_Genus
Bacillota
Eubacteriales
Raoultella planticola
Lacticaseibacillus rhamnosus
Klebsiella quasivariicola

Revision editor(s): Ayibatari