Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Yersin S, Garneau JR, Schneeberger PHH, Osman KA, Cercamondi CI, Muhummed AM, Tschopp R, Zinsstag J, Vonaesch P
Journal
Scientific reports
Year
2023
The composition and function of the intestinal microbiota are major determinants of human health and are strongly influenced by diet, antibiotic treatment, lifestyle and geography. Nevertheless, we currently have only little data on microbiomes of non-westernized communities. We assess the stool microbiota composition in 59 children aged 2-5 years from the Adadle district of Ethiopia, Somali Regional State. Here, milk and starch-rich food are predominant components of the local diet, where the inhabitants live a remote, traditional agropastoral lifestyle. Microbiota composition, function and the resistome were characterized by both 16S rRNA gene amplicon and shotgun metagenomic sequencing and compared to 1471 publicly available datasets from children living in traditional, transitional, and industrial communities with different subsistence strategies. Samples from the Adadle district are low in Bacteroidaceae, and Prevotellaceae, the main bacterial representatives in the feces of children living in industrialized and non-industrialized communities, respectively. In contrast, they had a higher relative abundance in Streptococcaceae, Bifidobacteriaceae and Erysipelatoclostridiaceae. Further, genes involved in degradation pathways of lactose, D-galactose and simple carbohydrates were enriched. Overall, our study revealed a unique composition of the fecal microbiota of these agropastoral children, highlighting the need to further characterize the fecal bacterial composition of human populations living different lifestyles.

Experiment 1


Needs review

Curated date: 2024/10/22

Curator: YokoC

Revision editor(s): YokoC

Subjects

Location of subjects
Ethiopia
Madagascar
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
Population Population,population
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Madagascar
Group 1 name Corresponds to the case (exposed) group for case-control studies
Adadle
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
2-5 year old children from the Adadle woreda district in Ethiopia, whose samples were sequenced using Primer 1 set (V4 501-508F/701-712R).
Group 0 sample size Number of subjects in the control (unexposed) group
431
Group 1 sample size Number of subjects in the case (exposed) group
54

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
LEfSe
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Signature 1

Needs review

Curated date: 2024/10/22

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 B

Description: LEfSe analysis using primer set 1 data showing ASV bacterial families associated with Adadle or Madagascar.

Abundance in Group 1: increased abundance in Adadle

NCBI Quality ControlLinks
Actinomycetaceae
Akkermansiaceae
Anaerovoracaceae
Atopobiaceae
Bacillaceae
Beijerinckiaceae
Bifidobacteriaceae
Carnobacteriaceae
Coprobacillaceae
Coriobacteriaceae
Eggerthellaceae
Enterococcaceae
Erysipelotrichaceae
Gemellaceae
Lachnospiraceae
Lactobacillaceae
Micrococcaceae
Monoglobaceae
Peptoniphilaceae
Peptostreptococcaceae
Pirellulaceae
Planococcaceae
Puniceicoccaceae
Staphylococcaceae
Streptococcaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/22

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 B

Description: LEfSe analysis using primer set 1 data showing ASV bacterial families associated with Adadle or Madagascar.

Abundance in Group 1: decreased abundance in Adadle

NCBI Quality ControlLinks
Acidaminococcaceae
Bacteroidaceae
Campylobacteraceae
Desulfovibrionaceae
Helicobacteraceae
Muribaculaceae
Mycoplasmataceae
Neisseriaceae
Oscillospiraceae
Pasteurellaceae
Prevotellaceae
Rikenellaceae
Selenomonadaceae
Succinivibrionaceae
Sutterellaceae
Veillonellaceae
[Eubacterium] coprostanoligenes group[Eubacterium] coprostanoligenes group
Oscillospirales UCG-010Oscillospirales UCG-010

Revision editor(s): YokoC

Experiment 2


Needs review

Curated date: 2024/10/22

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Central African Republic
Ethiopia


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Central African Republic
Group 0 sample size Number of subjects in the control (unexposed) group
274

Lab analysis

Statistical Analysis

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Signature 1

Needs review

Curated date: 2024/10/22

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 B

Description: LEfSe analysis using primer set 1 data showing bacterial families associated with Adadle or Central African Republic.

Abundance in Group 1: increased abundance in Adadle

NCBI Quality ControlLinks
Actinomycetaceae
Akkermansiaceae
Anaerovoracaceae
Atopobiaceae
Bacillaceae
Beijerinckiaceae
Bifidobacteriaceae
Carnobacteriaceae
Coprobacillaceae
Coriobacteriaceae
Eggerthellaceae
Enterobacteriaceae
Enterococcaceae
Erysipelotrichaceae
Eubacteriaceae
Gemellaceae
Lachnospiraceae
Lactobacillaceae
Micrococcaceae
Monoglobaceae
Peptoniphilaceae
Peptostreptococcaceae
Pirellulaceae
Planococcaceae
Rhizobiaceae
Staphylococcaceae
Streptococcaceae
ThioglobaceaeThioglobaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/22

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 B

Description: LEfSe analysis using primer set 1 data showing bacterial families associated with Adadle or Central African Republic.

Abundance in Group 1: decreased abundance in Adadle

NCBI Quality ControlLinks
Acholeplasmataceae
Acidaminococcaceae
Bacteroidaceae
Barnesiellaceae
Campylobacteraceae
Desulfovibrionaceae
Helicobacteraceae
Marinifilaceae
Muribaculaceae
Oscillospiraceae
Oxalobacteraceae
Pasteurellaceae
Prevotellaceae
Rikenellaceae
Selenomonadaceae
Sutterellaceae
Tannerellaceae
Veillonellaceae
[Eubacterium] coprostanoligenes group[Eubacterium] coprostanoligenes group
Oscillospirales UCG-010Oscillospirales UCG-010

Revision editor(s): YokoC

Experiment 3


Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Ethiopia
Sweden
United States of America


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Industrial Lifestyle
Group 1 name Corresponds to the case (exposed) group for case-control studies
Adadle Agropastoral Lifestyle
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
2-5 year old children from the Adadle woreda district in Ethiopia with an Agropastoral lifestyle, whose samples were sequenced using Primer 2 set (V4 515F/806R). Lifestyle classifications of the different populations were based on the publications used for the datasets.
Group 0 sample size Number of subjects in the control (unexposed) group
484
Group 1 sample size Number of subjects in the case (exposed) group
13

Lab analysis

Statistical Analysis

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Signature 1

Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 D

Description: LEfSe analysis showing bacterial families associated with agropastoral and industrial lifestyles.

Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Anaerovoracaceae
Atopobiaceae
Bacillaceae
Coprobacillaceae
Coriobacteriaceae
Enterococcaceae
Erysipelotrichaceae
Monoglobaceae
Prevotellaceae
Streptococcaceae
Succinivibrionaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 D

Description: LEfSe analysis showing bacterial families associated with agropastoral and industrial lifestyles.

Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Akkermansiaceae
Bacteroidaceae
Barnesiellaceae
Bifidobacteriaceae
Clostridiaceae
Defluviitaleaceae
Desulfovibrionaceae
Marinifilaceae
Oscillospiraceae
Pasteurellaceae
Peptostreptococcaceae
Porphyromonadaceae
Rikenellaceae
Sutterellaceae
Tannerellaceae
Veillonellaceae

Revision editor(s): YokoC

Experiment 4


Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Cameroon
China
Ethiopia
Malawi
Peru
United Republic of Tanzania
Venezuela


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Traditional Lifestyle
Group 0 sample size Number of subjects in the control (unexposed) group
107

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 D

Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a traditional lifestyle.

Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Anaerovoracaceae
Coprobacillaceae
Coriobacteriaceae
Eggerthellaceae
Enterobacteriaceae
Erysipelotrichaceae
Streptococcaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 D

Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a traditional lifestyle.

Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Acholeplasmataceae
Acidaminococcaceae
Bacteroidaceae
Campylobacteraceae
Clostridiaceae
Desulfovibrionaceae
Elusimicrobiaceae
Methanobacteriaceae
Muribaculaceae
Oscillospiraceae
Oxalobacteraceae
Pasteurellaceae
Prevotellaceae
Rikenellaceae
Selenomonadaceae
Spirochaetaceae
Succinivibrionaceae
Sutterellaceae
Tannerellaceae
Veillonellaceae
candidate division VadinBE97
Oscillospirales UCG-010Oscillospirales UCG-010

Revision editor(s): YokoC

Experiment 5


Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Bangladesh
El Salvador
Ethiopia
Peru


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Transitional Lifestyle
Group 0 sample size Number of subjects in the control (unexposed) group
88

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 D

Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a transitional lifestyle.

Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Bacillaceae
Carnobacteriaceae
Coprobacillaceae
Coriobacteriaceae
Erysipelotrichaceae
Leptotrichiaceae
Puniceicoccaceae
Streptococcaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/23

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S6 D

Description: LEfSe analysis showing bacterial families associated with children from an Adadle agropastoral lifestyle or with a transitional lifestyle.

Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Bifidobacteriaceae
Clostridiaceae
Lactobacillaceae
Oscillospiraceae
Peptostreptococcaceae
Veillonellaceae
Oscillospirales UCG-010Oscillospirales UCG-010

Revision editor(s): YokoC

Experiment 6


Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Ethiopia


Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
COPRO-seq COPRO-seq,cOPRO-seq
Group 0 name Corresponds to the control (unexposed) group for case-control studies
mOTUs2
Group 1 name Corresponds to the case (exposed) group for case-control studies
MetaPhlAn3
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
MetaPhlan3 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.
Group 0 sample size Number of subjects in the control (unexposed) group
15
Group 1 sample size Number of subjects in the case (exposed) group
15

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).
log transformation
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
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Not specified


Signature 1

Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S7 A

Description: Species with a significantly different abundance between the two profiling tools, mOTUs2 and MetaPhlAn3

Abundance in Group 1: increased abundance in MetaPhlAn3

NCBI Quality ControlLinks
Actinomyces oris
Actinomyces sp. HMSC035G02
Actinomyces sp. oral taxon 181
Agathobaculum butyriciproducens
Bacteroides uniformis
Collinsella intestinalis
Collinsella stercoris
Eggerthella lenta
Fusicatenibacter saccharivorans
Gemmiger formicilis
Parabacteroides distasonis
Roseburia sp. CAG:471
Ruthenibacterium lactatiformans
Slackia isoflavoniconvertens
[Collinsella] massiliensis

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S7 A

Description: Species with a significantly different abundance between the two profiling tools, mOTUs2 and MetaPhlAn3.

Abundance in Group 1: decreased abundance in MetaPhlAn3

NCBI Quality ControlLinks
Actinomyces dentalis
Actinomyces sp. ICM39
Actinomyces viscosus
Arachnia propionica
Blautia sp. KLE 1732
Candidatus Nanosynbacter lyticus
Senegalimassilia anaerobia
Streptococcus intermedius
Streptococcus sp. HSISM1
bacterium LF-3
unclassified Bacilli
unclassified Bacillota
unclassified Eggerthellaceae
unclassified Lachnospiraceae
unclassified Oscillospiraceae
unclassified Peptostreptococcaceae
uncultured Butyricicoccus sp.
uncultured Candidatus Saccharibacteria bacterium
uncultured Clostridium sp.
uncultured Collinsella sp.
uncultured Eubacterium sp.
uncultured Faecalibacterium sp.
uncultured Mogibacterium sp.
uncultured Prevotella sp.
uncultured Streptococcus sp.
uncultured Sutterella sp.
Eggerthella lenta [C Clostridioides difficile]Eggerthella lenta [C Clostridioides difficile]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
unknown Lactobacillalesunknown Lactobacillales
Streptococcus sp. [equinus/infantarius/lutetiensis]Streptococcus sp. [equinus/infantarius/lutetiensis]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
Streptococcus sp. [equinus/gallolyticus/macedonicus/pasteurianus]Streptococcus sp. [equinus/gallolyticus/macedonicus/pasteurianus]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
Streptococcus sp. [I-G2/I-P16]Streptococcus sp. [I-G2/I-P16]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
Actinomyces sp. [ICM58/oral taxon 172]Actinomyces sp. [ICM58/oral taxon 172]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
Actinomyces sp. [oral taxon 181/ph3]Actinomyces sp. [oral taxon 181/ph3]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
Bacteroides sp. [dorei/vulgatus]Bacteroides sp. [dorei/vulgatus]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
Bacteroides sp. [rodentium/uniformis]Bacteroides sp. [rodentium/uniformis]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">
Bifidobacterium sp. [catenulatum/kashiwanohense]Bifidobacterium sp. [catenulatum/kashiwanohense]<i class="fas text- fa-comment" title="The part "]" of the query was not understood.</br>Results might not be as expected. - Review">

Revision editor(s): YokoC

Experiment 7


Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Primer set 1
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
6

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8 B

Description: Significantly different families between primer set 1 and MetaPhlAn3.

Abundance in Group 1: increased abundance in MetaPhlAn3

NCBI Quality ControlLinks
Clostridiales Family XIII bacterium
Eubacteriaceae
unclassified Bacillales

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8 B

Description: Significantly different families between primer set 1 and MetaPhlAn3.

Abundance in Group 1: decreased abundance in MetaPhlAn3

NCBI Quality ControlLinks
Anaerovoracaceae
Butyricicoccaceae
Coprobacillaceae
Gemellaceae
[Eubacterium] coprostanoligenes group[Eubacterium] coprostanoligenes group

Revision editor(s): YokoC

Experiment 8


Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Primer set 2

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8 B

Description: Significantly different families between primer set 2 and MetaPhlAn3.

Abundance in Group 1: increased abundance in MetaPhlAn3

NCBI Quality ControlLinks
Clostridiales Family XIII bacterium
Corynebacteriaceae
Eubacteriaceae
Micrococcaceae
unclassified Bacillales

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/24

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8 B

Description: Significantly different families between primer set 2 and MetaPhlAn3.

Abundance in Group 1: decreased abundance in MetaPhlAn3

NCBI Quality ControlLinks
Anaerovoracaceae
Coprobacillaceae

Revision editor(s): YokoC

Experiment 9


Needs review

Curated date: 2024/10/25

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Primer set 1
Group 1 name Corresponds to the case (exposed) group for case-control studies
mOTUs2
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
mOTUs2 taxonomic profiling of shotgun metagenomic samples from Adadle woreda 2-5 year old children.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/25

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8 B

Description: Significantly different families between primer set 1 and mOTUs2.

Abundance in Group 1: increased abundance in mOTUs2

NCBI Quality ControlLinks
Eubacteriaceae
Eubacteriales incertae sedis
Gemellaceae
Propionibacteriaceae
unclassified Bacilli
unclassified Bacillota
unclassified Eubacteriales
uncultured Candidatus Saccharibacteria bacterium
Bacteria family incertae sedisBacteria family incertae sedis
unknown Lactobacillalesunknown Lactobacillales
Symbiobacteriaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/25

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8 B

Description: Significantly different families between primer set 1 and mOTUs2.

Abundance in Group 1: decreased abundance in mOTUs2

NCBI Quality ControlLinks
Anaerovoracaceae
Butyricicoccaceae
Coprobacillaceae
Gemellaceae
[Eubacterium] coprostanoligenes group[Eubacterium] coprostanoligenes group

Revision editor(s): YokoC

Experiment 10


Needs review

Curated date: 2024/10/25

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Primer set 2

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/25

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8 B

Description: Significantly different families between primer set 2 and mOTUS2.

Abundance in Group 1: increased abundance in mOTUs2

NCBI Quality ControlLinks
Clostridiaceae
Corynebacteriaceae
Eubacteriaceae
Gemellaceae
Micrococcaceae
Propionibacteriaceae
Sutterellaceae
Bacteria family incertae sedisBacteria family incertae sedis
unknown Lactobacillalesunknown Lactobacillales
Symbiobacteriaceae
Eubacteriales incertae sedis
unclassified Bacilli
uncultured Candidatus Saccharibacteria bacterium
unclassified Eubacteriales
unclassified Bacillota

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/25

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S8

Description: Significantly different families between primer set 2 and mOTUs2.

Abundance in Group 1: decreased abundance in mOTUs2

NCBI Quality ControlLinks
Anaerovoracaceae
Coprobacillaceae

Revision editor(s): YokoC

Experiment 11


Needs review

Curated date: 2024/10/30

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Central African Republic
Ethiopia
Madagascar


Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Population Population,population
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cluster P+
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cluster P-
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
One of two clusters based on bacterial taxa abundance, determined by the use of Euclidean distances and Ward's linkage method on data from primer 1 set.
Group 0 sample size Number of subjects in the control (unexposed) group
526
Group 1 sample size Number of subjects in the case (exposed) group
233

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances


Signature 1

Needs review

Curated date: 2024/10/31

Curator: YokoC

Revision editor(s): YokoC

Source: Figure 3 C

Description: Heatmap of the most abundant species with significantly different relative abundance between two clusters (P+ and P-) in the primer 1 set.

Abundance in Group 1: increased abundance in Cluster P-

NCBI Quality ControlLinks
Bifidobacterium catenulatum
Blautia obeum
Collinsella aerofaciens
Roseburia inulinivorans
Streptococcus lutetiensis
uncultured Prevotella sp.
uncultured Prevotellaceae bacterium
Escherichia/Shigella coliEscherichia/Shigella coli
Erysipelotrichaceae UCG-003Erysipelotrichaceae UCG-003
uncultured Candidatus Bacilliplasmauncultured Candidatus Bacilliplasma

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/10/31

Curator: YokoC

Revision editor(s): YokoC

Source: Figure 3C

Description: Heatmap of the most abundant species with significantly different relative abundance between two clusters (P+ and P-) in the primer 1 set.

Abundance in Group 1: decreased abundance in Cluster P-

NCBI Quality ControlLinks
Leyella stercorea
uncultured Alloprevotella sp.
uncultured Dialister sp.
uncultured Succinivibrio sp.
uncultured Prevotella 9uncultured Prevotella 9
Prevotella 9 copriPrevotella 9 copri
uncultured Phascolarctobacterium sp.uncultured Phascolarctobacterium sp.

Revision editor(s): YokoC

Experiment 12


Needs review

Curated date: 2024/10/31

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Signature 1

Needs review

Curated date: 2024/10/31

Curator: YokoC

Revision editor(s): YokoC

Source: Figure 3C

Description: Heatmap of the most abundant species with significantly different relative abundance between two clusters (P9+ and P9−).

Abundance in Group 1: increased abundance in Cluster P-

NCBI Quality ControlLinks
Anaerostipes hadrus
Bacteroides fragilis
Bacteroides ovatus
Bacteroides uniformis
Bifidobacterium catenulatum
Blautia obeum
Dialister invisus
Roseburia inulinivorans
Ruminococcus bromii
uncultured Alloprevotella sp.
uncultured Blautia sp.
uncultured Dialister sp.
uncultured Faecalibacterium sp.
uncultured Prevotella sp.
uncultured Prevotellaceae bacterium
Escherichia/Shigella coliEscherichia/Shigella coli
Uncultured FusicatenibacterUncultured Fusicatenibacter
UCG-002UCG-002

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/11/01

Curator: YokoC

Revision editor(s): YokoC

Source: Figure 3C

Description: Heatmap of the most abundant species with significantly different relative abundance between two clusters (P9+ and P9−).

Abundance in Group 1: decreased abundance in Cluster P-

NCBI Quality ControlLinks
uncultured Succinivibrio sp.
uncultured Prevotella 9uncultured Prevotella 9
Prevotella 9 copriPrevotella 9 copri

Revision editor(s): YokoC

Experiment 13


Needs review

Curated date: 2024/11/01

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Ethiopia
United States of America


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Industrial Lifestyle
Group 1 name Corresponds to the case (exposed) group for case-control studies
Adadle Agropastoral Lifestyle
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
2-5 year old children from the Adadle woreda district in Ethiopia with an agropastoral lifestyle, whose samples were taxonomically profiled using mOTUs2.
Group 0 sample size Number of subjects in the control (unexposed) group
15
Group 1 sample size Number of subjects in the case (exposed) group
29

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).
log transformation


Signature 1

Needs review

Curated date: 2024/11/02

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Erysipelotrichaceae
Lactobacillaceae
Prevotellaceae
Streptococcaceae
Succinivibrionaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/11/02

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Bacteroidaceae

Revision editor(s): YokoC

Experiment 14


Needs review

Curated date: 2024/11/02

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Ethiopia
Peru
United Republic of Tanzania
Zimbabwe


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Traditional Lifestyle
Group 1 sample size Number of subjects in the case (exposed) group
40

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/11/03

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Bifidobacteriaceae
Erysipelotrichaceae
Lactobacillaceae
Streptococcaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/11/03

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Bacteroidaceae
Prevotellaceae
Succinivibrionaceae

Revision editor(s): YokoC

Experiment 15


Needs review

Curated date: 2024/11/03

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
El Salvador
Ethiopia
Peru


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Transitional Lifestyle
Group 0 sample size Number of subjects in the control (unexposed) group
18
Group 1 sample size Number of subjects in the case (exposed) group
15

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: increased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Erysipelotrichaceae
Lactobacillaceae
Streptococcaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: decreased abundance in Adadle Agropastoral Lifestyle

NCBI Quality ControlLinks
Bifidobacteriaceae
Prevotellaceae
Bacteroidaceae

Revision editor(s): YokoC

Experiment 16


Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
Ethiopia
Peru
United Republic of Tanzania
Zimbabwe
United States of America


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Industrial Lifestyle
Group 1 name Corresponds to the case (exposed) group for case-control studies
Traditional Lifestyle
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
2-5 year old children with a traditional lifestyle, whose samples were taxonomically profiled using mOTUs2.
Group 0 sample size Number of subjects in the control (unexposed) group
29
Group 1 sample size Number of subjects in the case (exposed) group
40

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: increased abundance in Traditional Lifestyle

NCBI Quality ControlLinks
Prevotellaceae
Succinivibrionaceae
Lactobacillaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: decreased abundance in Traditional Lifestyle

NCBI Quality ControlLinks
Akkermansiaceae
Bacteroidaceae
Bifidobacteriaceae

Revision editor(s): YokoC

Experiment 17


Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
El Salvador
Ethiopia
Peru
United States of America


Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
2-5 year old children with a transitional lifestyle, whose samples were taxonomically profiled using mOTUs2.
Group 1 sample size Number of subjects in the case (exposed) group
18

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: increased abundance in Traditional Lifestyle

NCBI Quality ControlLinks
Bifidobacteriaceae
Prevotellaceae
Succinivibrionaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: decreased abundance in Traditional Lifestyle

NCBI Quality ControlLinks
Bacteroidaceae
Lactobacillaceae

Revision editor(s): YokoC

Experiment 18


Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Location of subjects
El Salvador
Peru
United Republic of Tanzania
Zimbabwe


Group 0 name Corresponds to the control (unexposed) group for case-control studies
Traditional Lifestyle
Group 1 name Corresponds to the case (exposed) group for case-control studies
Transitional Lifestyle
Group 0 sample size Number of subjects in the control (unexposed) group
40

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: increased abundance in Transitional Lifestyle

NCBI Quality ControlLinks
Bifidobacteriaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2024/11/04

Curator: YokoC

Revision editor(s): YokoC

Source: Figure S9 B

Description: Significantly different relative abundances of bacterial families in the BloSSUM (Bloom or selected in societies of urbanization/modernization) or VANISH (Volatile and/or associated negatively with industrialized societies of humans) categories and those with higher relative abundance in Adadle woreda.

Abundance in Group 1: decreased abundance in Transitional Lifestyle

NCBI Quality ControlLinks
Prevotellaceae
Succinivibrionaceae

Revision editor(s): YokoC