Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C, Wilmes P
Journal
Frontiers in microbiology
Year
2017
Keywords:
amplicon sequencing, delivery mode, fungi, infant gut microbiome, microbial colonization, quantitative real-time PCR, succession
Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.

Experiment 1


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Subjects

Location of subjects
Luxembourg
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 at day 3
Group 1 name Corresponds to the case (exposed) group for case-control studies
c-section
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
meconium samples were collected at day 1 after delivery
Group 0 sample size Number of subjects in the control (unexposed) group
6
Group 1 sample size Number of subjects in the case (exposed) group
3
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
increased
Richness Number of species
increased

Signature 1

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 7 and Fig. S4

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: increased abundance in c-section

NCBI Quality ControlLinks
Staphylococcus
Lactobacillus

Revision editor(s): WikiWorks

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Aiyshaaaa, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
vaginal delivery at day 5
Group 0 sample size Number of subjects in the control (unexposed) group
7
Group 1 sample size Number of subjects in the case (exposed) group
5

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.01

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged

Signature 1

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 6S

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: increased abundance in c-section

NCBI Quality ControlLinks
Bacillota

Revision editor(s): WikiWorks

Signature 2

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 6S

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: decreased abundance in c-section

NCBI Quality ControlLinks
Bacteroidota

Revision editor(s): WikiWorks

Experiment 3


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
vaginal delivery at day 28
Group 1 sample size Number of subjects in the case (exposed) group
6

Lab analysis

Statistical Analysis

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
unchanged

Signature 1

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 6S and Fig. S4

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: decreased abundance in c-section

NCBI Quality ControlLinks
Bacteroidota
Bacteroides

Revision editor(s): WikiWorks

Experiment 4


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
vaginal delivery at day 150
Group 0 sample size Number of subjects in the control (unexposed) group
6
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged

Signature 1

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 6S

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: decreased abundance in c-section

NCBI Quality ControlLinks
Bacteroidota
Bacteroides

Revision editor(s): WikiWorks

Experiment 5


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
vaginal delivery at day 365
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

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Richness Number of species
unchanged

Signature 1

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 6S

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: decreased abundance in c-section

NCBI Quality ControlLinks
Bacteroidota

Revision editor(s): WikiWorks

Experiment 6


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Premature birth Birth, Premature,Birth, Preterm,Births, Premature,Births, Preterm,Premature Births,Preterm Birth,Preterm Births,Premature birth,premature birth
Group 0 name Corresponds to the control (unexposed) group for case-control studies
full-term delivery >39 weeks at day 3
Group 1 name Corresponds to the case (exposed) group for case-control studies
late preterm 34-36 weeks
Group 0 sample size Number of subjects in the control (unexposed) group
4

Lab analysis

Statistical Analysis

Statistical test
Kruskall-Wallis
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.01


Signature 1

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: text pg11 and figure 7s

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: decreased abundance in late preterm 34-36 weeks

NCBI Quality ControlLinks
Bacteroidota

Revision editor(s): WikiWorks

Experiment 7


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

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
Group 1 name Corresponds to the case (exposed) group for case-control studies
overall time point infants samples of c-section
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
7

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05


Signature 1

Reviewed Marked as Reviewed by Fatima on 2021/08/9

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Fatima, WikiWorks

Source: supplemantry file 9

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: increased abundance in overall time point infants samples of c-section

NCBI Quality ControlLinks
Akkermansia
Anaerostipes
Clostridium
Dialister
Enterobacter
Enterococcus
Flavonifractor
Gemella
Haemophilus
Lactobacillus
Propionibacterium
Rothia
Staphylococcus
Streptococcus
unclassified Lachnospiraceae

Revision editor(s): Fatima, WikiWorks

Signature 2

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: supplemantry file 9

Description: qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.

Abundance in Group 1: decreased abundance in overall time point infants samples of c-section

NCBI Quality ControlLinks
Parabacteroides
Bacteroides
Alistipes

Revision editor(s): WikiWorks

Experiment 8


Reviewed Marked as Reviewed by Lwaldron on 2022/03/2

Curated date: 2022/03/02

Curator: Shaimaa

Revision editor(s): Lwaldron, Shaimaa, WikiWorks, Aiyshaaaa

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Meconium Meconium,meconium
Group 1 name Corresponds to the case (exposed) group for case-control studies
C-section
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Not specified
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
6
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
11 mothers (6 controls and 5 cases) used antibiotics 12 hours before and after delivery, 3 VD mothers were positive group B Streptococcus screening.

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
increased