Comparison of changes in fecal microbiota of calves with and without dam

From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM, Peng Q
Journal
PeerJ
Year
2022
Keywords:
Calf, Cultivation method, Dynamics, Microbial community
In pastoral areas and semi-agricultural and semi-pastoral areas of Sichuan, beef cattle breeding mode is mainly dependent on nature to raise livestock. On the one hand, owing to the shortage of forage grass in spring, cows suffer from malnutrition. On the other hand, competition for milk between human and livestock further deepens the malnutrition of newborn calves, and the mortality rate even exceeds 40%, resulting in serious waste of beef cattle source resources. The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome. Sixteen healthy calves (Yak ♂ × Pian cattle ♀, with similar birthday 0 ± 2 d and body weight 13.1 ± 1.13 kg), were selected and randomly divided into two groups. The control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the whole 95 days formal experimental period. Fecal samples were collected on 35, 65 and 95 days of age for high-throughput sequencing. The α-diversity was different between the two groups on day 35; however, the bacterial species richness and diversity was almost not different on day 95. Principal coordinates analysis revealed significant difference between the two groups on all the three time points, and the timepoints of day 65 and 95 were closer and separated from the timepoints of day 35 in calves with dam, whereas the timepoints of day 35 and 65 were closer and separated from day 95 in calves without dam. As time passed, the abundance of Firmicutes increased, while Proteobacteria and Actinobacteria decreased in calves with dam. But in calves without dam, the abundance of Bacteroidetes and Proteobacteria increased on day 65 and then decreased on day 95. In genus level, the relative abundance of Bacteroides decreased in calf with dam while its abundance increased first and then decreased in calf without dam but both resulted in the range of 3.5~4.5%. The relative abundance of Lactobacillus decreased, whereas Ruminococcaceae UCG-005 increased in both groups as the calf grew up. It was concluded that the richness and evenness of the microbial communities was higher in calves with dam than without dam, and a stable gut microbiome in calve with dam is established earlier than calf without dam.

Experiment 1


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/03

Curator: Folakunmi

Revision editor(s): Folakunmi

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Bos grunniens
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
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Calves with dam on day 35
Group 1 name Corresponds to the case (exposed) group for case-control studies
Calves without dam on day 35
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Calves without dam on day 35 of the whole 95 days formal experimental period.
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
8
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
none

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/03

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.

Abundance in Group 1: increased abundance in Calves without dam on day 35

NCBI Quality ControlLinks
Actinomycetota
Myroides
Paraeggerthella
Peptostreptococcus

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/04

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 35 of experiment, and calves without dam at day 35 of experiment.

Abundance in Group 1: decreased abundance in Calves without dam on day 35

NCBI Quality ControlLinks
Bacteroides
Escherichia/Shigella sp.
Parabacteroides

Revision editor(s): Folakunmi

Experiment 2


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21

Curated date: 2023/11/03

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Calves with dam on day 65
Group 1 name Corresponds to the case (exposed) group for case-control studies
Calves without dam on day 65
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Calves without dam on day 65 of the whole 95 days formal experimental period.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21

Curated date: 2023/11/04

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.

Abundance in Group 1: increased abundance in Calves without dam on day 65

NCBI Quality ControlLinks
Bacteroides
Lactobacillus
unclassified Oscillospiraceae

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21

Curated date: 2023/11/04

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 65 of experiment, and calves without dam at day 65 of experiment.

Abundance in Group 1: decreased abundance in Calves without dam on day 65

NCBI Quality ControlLinks
Ruminococcaceae bacterium UCG-005
Treponema
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group
unclassified Oscillospiraceae

Revision editor(s): Folakunmi

Experiment 3


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-21

Curated date: 2023/11/03

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Calves with dam on day 95
Group 1 name Corresponds to the case (exposed) group for case-control studies
Calves without dam on day 95
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Calves without dam on day 95 of the whole 95 days formal experimental period.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/04

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.

Abundance in Group 1: increased abundance in Calves without dam on day 95

NCBI Quality ControlLinks
Eubacterium coprostanoligenes
Treponema

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/11/04

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Figures 5&6

Description: Differentially abundant taxa between calves with dam at day 95 of experiment, and calves without dam at day 95 of experiment.

Abundance in Group 1: decreased abundance in Calves without dam on day 95

NCBI Quality ControlLinks
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group
Ruminococcaceae bacterium UCG-005

Revision editor(s): Folakunmi