Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-6
study design
case-control
Citation
PMID PubMed identifier for scientific articles.
37428087
DOI Digital object identifier for electronic documents.
https://doi.org/10.1128/spectrum.00590-23
URI
https://journals.asm.org/doi/10.1128/spectrum.00590-23
Authors
Bai H, Liu T, Wang S, Gong W, Shen L, Zhang S, Wang Z
Journal
Microbiology spectrum
Year
2023
Keywords:
QIIME2, acute diarrhea, domestic cat, gut microbiota, metabolome, microbiome
Changes in diet and environment can lead to acute diarrhea in companion animals, but the composition and interactions of the gut microbiome during acute diarrhea remain unclear. In this multicenter case-control study, we investigated the relationship between intestinal flora and acute diarrhea in two breeds of cats. Acutely diarrheic American Shorthair (MD, n = 12) and British Shorthair (BD, n = 12) and healthy American Shorthair (MH, n = 12) and British Shorthair (BH, n = 12) cats were recruited. Gut microbial 16S rRNA sequencing, metagenomic sequencing, and untargeted metabolomic analysis were performed. We observed significant differences in beta-diversity (Adonis, P < 0.05) across breeds and disease state cohorts. Profound differences in gut microbial structure and function were found between the two cat breeds. In comparison to healthy British Shorthair cats, Prevotella, Providencia, and Sutterella were enriched while Blautia, Peptoclostridium, and Tyzzerella were reduced in American Shorthair cats. In the case-control cohort, cats with acute diarrhea exhibited an increased abundance of Bacteroidota, Prevotella, and Prevotella copri and a decreased abundance of Bacilli, Erysipelotrichales, and Erysipelatoclostridiaceae (both MD and BD cats, P < 0.05). Metabolomic analysis identified significant changes in the BD intestine, affecting 45 metabolic pathways. Moreover, using a random forest classifier, we successfully predicted the occurrence of acute diarrhea with an area under the curve of 0.95. Our findings indicate a distinct gut microbiome profile that is associated with the presence of acute diarrhea in cats. However, further investigations using larger cohorts of cats with diverse conditions are required to validate and extend these findings. IMPORTANCE Acute diarrhea is common in cats, and our understanding of the gut microbiome variations across breeds and disease states remains unclear. We investigated the gut microbiome of two cat breeds (British Shorthair and American Shorthair) with acute diarrhea. Our study revealed significant effects of breeds and disease states on the structure and function of the gut microbiota in cats. These findings emphasize the need to consider breed-related factors in animal nutrition and research models. Additionally, we observed an altered gut metabolome in cats with acute diarrhea, closely linked to changes in bacterial genera. We identified a panel of microbial biomarkers with high diagnostic accuracy for feline acute diarrhea. These findings provide novel insights into the diagnosis, classification, and treatment of feline gastrointestinal diseases.

Experiment 1


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Curated date: 2024/03/12

Curator: Imaspecial

Revision editor(s): Imaspecial, Scholastica

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Felis catus
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
Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy American Shorthair (MH)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Acutely diarrheic American Shorthair cats (MD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
American Shorthair cats with acute diarrhea
Group 0 sample size Number of subjects in the control (unexposed) group
12
Group 1 sample size Number of subjects in the case (exposed) group
12
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

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
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
4

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
increased

Signature 1

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Curated date: 2024/03/12

Curator: Imaspecial

Revision editor(s): Imaspecial, Scholastica

Source: FIG 3a

Description: Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using LEfSe

Abundance in Group 1: increased abundance in Acutely diarrheic American Shorthair cats (MD)

NCBI Quality ControlLinks
Bacteroidales   
Bacteroidia   
Bacteroidota   
Prevotella   
Prevotellaceae   
Segatella copri   

Revision editor(s): Imaspecial, Scholastica

Signature 2

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Curated date: 2024/03/12

Curator: Imaspecial

Revision editor(s): Imaspecial, Scholastica

Source: FIG 3a

Description: Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using LEfSe

Abundance in Group 1: decreased abundance in Acutely diarrheic American Shorthair cats (MD)

NCBI Quality ControlLinks
Bacilli   
Bacillota   
Catenibacterium   
Dialister   
Erysipelotrichaceae   
Erysipelotrichales   
Negativicutes   
Selenomonadales   
Solobacterium   
Veillonellaceae   
Veillonellales   
ErysipelatoclostridiaceaeErysipelatoclostridiaceae

Revision editor(s): Imaspecial, Scholastica

Experiment 2


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Needs review

Curated date: 2024/03/12

Curator: Imaspecial

Revision editor(s): Imaspecial, Scholastica

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy British Shorthair (BH)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Acutely diarrheic British Shorthair cats (BD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
British Shorthair cats with acute diarrhea

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
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Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/03/12

Curator: Imaspecial

Revision editor(s): Imaspecial, Scholastica

Source: FIG 3c

Description: Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe

Abundance in Group 1: increased abundance in Acutely diarrheic British Shorthair cats (BD)

NCBI Quality ControlLinks
Bacteroidales   
Bacteroidia   
Bacteroidota   
Prevotella   
Prevotellaceae   
Segatella copri   

Revision editor(s): Imaspecial, Scholastica

Signature 2

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Curated date: 2024/03/12

Curator: Imaspecial

Revision editor(s): Imaspecial, Scholastica

Source: FIG 3c

Description: Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe

Abundance in Group 1: decreased abundance in Acutely diarrheic British Shorthair cats (BD)

NCBI Quality ControlLinks
Actinomycetota   
Atopobiaceae   
Bacilli   
Butyricicoccaceae   
Collinsella   
Collinsella tanakaei   
Coriobacteriaceae   
Coriobacteriales   
Coriobacteriia   
Erysipelotrichales   
Parolsenella   
Thomasclavelia   
Thomasclavelia spiroformis   
ErysipelatoclostridiaceaeErysipelatoclostridiaceae

Revision editor(s): Imaspecial, Scholastica

Experiment 3


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Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Lab analysis

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

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
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Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: FIG 3e

Description: Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe

Abundance in Group 1: increased abundance in Acutely diarrheic British Shorthair cats (BD)

NCBI Quality ControlLinks
Prevotella   
Segatella copri CAG:164   

Revision editor(s): Scholastica

Signature 2

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Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: FIG 3e

Description: Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using LEfSe

Abundance in Group 1: decreased abundance in Acutely diarrheic British Shorthair cats (BD)

NCBI Quality ControlLinks
Collinsella intestinalis   

Revision editor(s): Scholastica

Experiment 4


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Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Breed animal breed,Breed,breed
Group 1 name Corresponds to the case (exposed) group for case-control studies
Healthy American Shorthair (MH)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Healthy American Shorthair (MH) cats

Lab analysis

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

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: FIG 2a

Description: Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using LEfSe

Abundance in Group 1: increased abundance in Healthy American Shorthair (MH)

NCBI Quality ControlLinks
Bacteroidales   
Bacteroidia   
Bacteroidota   
Enterobacterales   
Gammaproteobacteria   
Morganellaceae   
Prevotella   
Prevotellaceae   
Providencia   
Pseudomonadota   
Segatella copri   

Revision editor(s): Scholastica

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: FIG 2a

Description: Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using LEfSe

Abundance in Group 1: decreased abundance in Healthy American Shorthair (MH)

NCBI Quality ControlLinks
Bacillota   
Blautia   
Blautia glucerasea   
Clostridia   
Cyanobacteriota   
Lachnospiraceae   
Lachnospirales   
Oscillospiraceae   
Peptoclostridium   
Peptostreptococcaceae   
Peptostreptococcales   
Staphylococcaceae   
Staphylococcus   
Tissierellales   
[Clostridium] colinum   
UBA1819UBA1819
StaphylococcalesStaphylococcales

Revision editor(s): Scholastica

Experiment 5


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Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Statistical test
Metastats
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Not specified

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
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Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Table S3

Description: Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using Metastat

Abundance in Group 1: increased abundance in Healthy American Shorthair (MH)

NCBI Quality ControlLinks
Bacteroidota   
Pseudomonadota   
Halobacteria   
Prevotella   
Providencia   
Sutterella   
Megasphaera   

Revision editor(s): Scholastica

Signature 2

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Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Table S3

Description: Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using Metastat

Abundance in Group 1: decreased abundance in Healthy American Shorthair (MH)

NCBI Quality ControlLinks
Bacillota   
Thermodesulfobacteriota   
Cyanobacteriota   
Verrucomicrobiota   
Planctomycetota   
Armatimonadota   
Blautia   
Peptoclostridium   
Tyzzerella   
Sarcina   
Anaerobutyricum hallii   
Butyricicoccus   
Fusicatenibacter   
Acinetobacter   
Bacillus   
UBA1819UBA1819
Staphylococcus   
Anaerofustis   

Revision editor(s): Scholastica

Experiment 6


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Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy American Shorthair (MH)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Acutely diarrheic American Shorthair cats (MD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
American Shorthair cats with acute diarrhea

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
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
increased

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Table S3

Description: Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using Metastat

Abundance in Group 1: increased abundance in Acutely diarrheic American Shorthair cats (MD)

NCBI Quality ControlLinks
Bacteroidota   
Acidobacteriota   
Thermodesulfobacteriota   
Gemmatimonadota   
Chloroflexia   
Myxococcota   
Prevotella   
Muribaculaceae   
Ralstonia   
uncultured Prevotellaceae bacterium   
Muribaculum   
Bacillus   
NK4A214 groupNK4A214 group
Thermoanaerobaculaceae bacterium   
Blastococcus   
S085S085
IMCC26256IMCC26256
Vicinamibacteria bacterium   
Arenimonas   
Skermanella   

Revision editor(s): Scholastica

Signature 2

EditHistoryDelete
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Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Table S3

Description: Species analysis of differences in healthy (MH) versus acutely diarrheic (MD) American Shorthair cats using Metastat

Abundance in Group 1: decreased abundance in Acutely diarrheic American Shorthair cats (MD)

NCBI Quality ControlLinks
Bacillota   
Solobacterium   
Catenibacterium   
Tyzzerella   
Parolsenella   
Catenisphaera   
Anaerovoracaceae bacterium   
Intestinimonas   

Revision editor(s): Scholastica

Experiment 7


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Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy British Shorthair (BH)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Acutely diarrheic British Shorthair cats (BD)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
British Shorthair cats with acute diarrhea

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
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Table S3

Description: Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using Metastat

Abundance in Group 1: increased abundance in Acutely diarrheic British Shorthair cats (BD)

NCBI Quality ControlLinks
Acidobacteriota   
Bacteroidota   
Prevotella   

Revision editor(s): Scholastica

Signature 2

EditHistoryDelete
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Your review change was submitted
Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: Supplementary Table S3

Description: Species analysis of differences in healthy (BH) versus acutely diarrheic (BD) British Shorthair cats using Metastat

Abundance in Group 1: decreased abundance in Acutely diarrheic British Shorthair cats (BD)

NCBI Quality ControlLinks
Actinomycetota   
Planctomycetota   
Armatimonadota   
Collinsella   
Thomasclavelia   
Parolsenella   

Revision editor(s): Scholastica

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