Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-30
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG, Fang MY
Journal
BMC microbiology
Year
2023
Keywords:
16S rDNA, Gut microbiota, Metagenomics, Tan sheep
The biological mechanisms underlying meat quality remain unclear. Currently, many studies report that the gastrointestinal microbiota is essential for animal growth and performance. However, it is uncertain which bacterial species are specifically associated with the meat quality traits. In this study, 16S rDNA and metagenomic sequencing were performed to explore the composition and function of microbes in various gastrointestinal segments of Tan sheep and Dorper sheep, as well as the relationship between microbiota and meat quality (specifically, the fatty acid content of the muscle). In the ruminal, duodenal, and colonic microbiome, several bacteria were uniquely identified in respective breeds, including Agrobacterium tumefaciens, Bacteroidales bacterium CF, and several members of the family Oscillospiraceae. The annotation of GO, KEGG, and CAZYme revealed that these different bacterial species were linked to the metabolism of glucose, lipids, and amino acids. Additionally, our findings suggested that 16 microbial species may be essential to the content of fatty acids in the muscle, especially C12:0 (lauric acid). 4 bacterial species, including Achromobacter xylosoxidans, Mageeibacillus indolicus, and Mycobacterium dioxanotrophicus, were positively correlated with C12:0, while 13 bacteria, including Methanobrevibacter millerae, Bacteroidales bacterium CF, and Bacteroides coprosuis were negatively correlated with C12:0. In a word, this study provides a basic data for better understanding the interaction between ruminant gastrointestinal microorganisms and the meat quality traits of hosts.

Experiment 1


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Ovis aries
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Rumen Paunch,Rumen,rumen
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Rumen of Dorper sheep (D_R)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Rumen of Tan Sheep (T_R)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Rumen of Tan sheep bred in Ningxia, China
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
4
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
No antibiotics during the experiment period

Lab analysis

Sequencing type
WMS
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
Illumina

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
2


Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Fig. 3A

Description: LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from metagenomic data at the species level.

Abundance in Group 1: increased abundance in Rumen of Tan Sheep (T_R)

NCBI Quality ControlLinks
Achromobacter xylosoxidans
Faecalibacterium prausnitzii
Flavonifractor plautii
Mageeibacillus indolicus
Oscillibacter sp. PEA192
Stenotrophomonas maltophilia
Stutzerimonas stutzeri

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Fig. 3A

Description: LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from metagenomic data at the species level.

Abundance in Group 1: decreased abundance in Rumen of Tan Sheep (T_R)

NCBI Quality ControlLinks
Methanobrevibacter millerae
Methanosphaera sp. BMS

Revision editor(s): Scholastica

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Duodenum of Dorper sheep (D_Du)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Duodenum of Tan Sheep (T_Du)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Duodenum of Tan sheep bred in Ningxia, China
Group 0 sample size Number of subjects in the control (unexposed) group
3
Group 1 sample size Number of subjects in the case (exposed) group
3

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Fig. 4A

Description: LEfSe analysis of differences in duodenal microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.

Abundance in Group 1: increased abundance in Duodenum of Tan Sheep (T_Du)

NCBI Quality ControlLinks
Agrobacterium tumefaciens
Arthrobacter alpinus
Friedmanniella luteola
Modestobacter marinus
Mycobacterium dioxanotrophicus
Ornithinimicrobium avium

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Fig. 4A

Description: LEfSe analysis of differences in duodenal microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.

Abundance in Group 1: decreased abundance in Duodenum of Tan Sheep (T_Du)

NCBI Quality ControlLinks
Advenella mimigardefordensis
Nostoc sphaeroides
Solibacillus silvestris

Revision editor(s): Scholastica

Experiment 3


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colon of Dorper sheep (D_Co)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colon of Tan Sheep (T_Co)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colon of Tan sheep bred in Ningxia, China
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
4

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Fig. 5A

Description: LEfSe analysis of differences in colonic microbial composition in Tan sheep versus Dorper sheep from metagenomic data at the species level.

Abundance in Group 1: decreased abundance in Colon of Tan Sheep (T_Co)

NCBI Quality ControlLinks
Acetivibrio thermocellus
Bacillus subtilis
Bacteroidales bacterium CF
Bacteroides coprosuis
Chryseobacterium gallinarum
Corynebacterium efficiens
Corynebacterium humireducens
Corynebacterium marinum
Dietzia lutea
Herbinix luporum
Mucilaginibacter mallensis
Mucinivorans hirudinis
Paenibacillus sp. FSL H7-0737
Parabacteroides distasonis
Rhodococcus rhodochrous
Selenomonas ruminantium
Solitalea canadensis
Streptococcus mutans

Revision editor(s): Scholastica

Experiment 4


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Rumen Paunch,Rumen,rumen
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Rumen of Dorper sheep (D_R)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Rumen of Tan Sheep (T_R)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Rumen of Tan sheep bred in Ningxia, China
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

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S6

Description: LEfSe analysis of ruminal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: increased abundance in Rumen of Tan Sheep (T_R)

NCBI Quality ControlLinks
Lachnospiraceae bacterium CG2
Papillibacter
Saccharofermentans
uncultured Prevotellaceae bacterium
Lachnospiraceae AC2004 groupLachnospiraceae AC2004 group

Revision editor(s): Scholastica

Experiment 5


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Duodenum of Dorper sheep (D_Du)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Duodenum of Tan Sheep (T_Du)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Duodenum of Tan sheep bred in Ningxia, China

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S7

Description: LEfSe analysis of duodenal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: increased abundance in Duodenum of Tan Sheep (T_Du)

NCBI Quality ControlLinks
Candidatus Gastranaerophilales
Candidatus Melainabacteria
Peptococcaceae
Saccharofermentans
Senegalimassilia
uncultured Lachnospiraceae bacterium

Revision editor(s): Scholastica

Experiment 6


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Jejunum of Dorper sheep (D_J)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Jejunum of Tan Sheep (T_J)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Jejunum of Tan sheep bred in Ningxia, China

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S8

Description: LEfSe analysis of jejunal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: increased abundance in Jejunum of Tan Sheep (T_J)

NCBI Quality ControlLinks
uncultured Prevotellaceae bacterium

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S8

Description: LEfSe analysis of jejunal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: decreased abundance in Jejunum of Tan Sheep (T_J)

NCBI Quality ControlLinks
Bacillales
Bacilli

Revision editor(s): Scholastica

Experiment 7


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colon of Dorper sheep (D_Co)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colon of Tan Sheep (T_Co)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colon of Tan sheep bred in Ningxia, China

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S9

Description: LEfSe analysis of colonic microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: increased abundance in Colon of Tan Sheep (T_Co)

NCBI Quality ControlLinks
Candidatus Gastranaerophilales
Candidatus Melainabacteria
Cyanobacteriota
Victivallis
uncultured Oscillospiraceae bacterium

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S9

Description: LEfSe analysis of colonic microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: decreased abundance in Colon of Tan Sheep (T_Co)

NCBI Quality ControlLinks
Bacteria
Rikenellaceae
uncultured Bacteroidales bacterium
uncultured Lachnospiraceae bacterium
Lachnoclostridium_10Lachnoclostridium_10
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group

Revision editor(s): Scholastica

Experiment 8


Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Cecum of Dorper sheep (D_C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cecum of Tan Sheep (T_C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Cecum of Tan sheep bred in Ningxia, China

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S10

Description: LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: increased abundance in Cecum of Tan Sheep (T_C)

NCBI Quality ControlLinks
Pseudomonadota
uncultured Oscillospiraceae bacterium

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-30

Curated date: 2024/04/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Fig. S10

Description: LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.

Abundance in Group 1: decreased abundance in Cecum of Tan Sheep (T_C)

NCBI Quality ControlLinks
Actinomycetota

Revision editor(s): Scholastica