Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-10-25

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

37375044

DOI Digital object identifier for electronic documents.

https://doi.org/10.3390/microorganisms11061542

URI

https://www.mdpi.com/2076-2607/11/6/1542

Authors

Scarafile D, Luise D, Motta V, Spiezio C, Modesto M, Porcu MM, Yitzhak Y, Correa F, Sandri C, Trevisi P, Mattarelli P

Journal

Microorganisms

Year

2023

Keywords:

Potamocherus porcus, beneficial microbes, bifidobacteria, diet, gut microbiota

Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype. As the name suggests, the Red River Hog is a wild member of the pig family living in Africa, in particular through the West and Central African rainforest. To date, very few studies have analysed the gut microbiota of Red River Hogs (RRHs) both housed under controlled conditions and in wild habitats. This study analysed the intestinal microbiota and the distribution of Bifidobacterium species in five Red River Hog (RRH) individuals (four adults and one juvenile), hosted in two different modern zoological gardens (Parco Natura Viva, Verona, and Bioparco, Rome) with the aim of disentangling the possible effects of captive different lifestyle and host genetics. Faecal samples were collected and studied both for bifidobacterial counts and isolation by means of culture-dependent method and for total microbiota analysis through the high-quality sequences of the V3-V4 region of bacterial 16S rRNA. Results showed a host-specific bifidobacterial species distribution. Indeed, B. boum and B. thermoacidophilum were found only in Verona RRHs, whereas B. porcinum species were isolated only in Rome RRHs. These bifidobacterial species are also typical of pigs. Bifidobacterial counts were about 106 CFU/g in faecal samples of all the individuals, with the only exception for the juvenile subject, showing 107 CFU/g. As in human beings, in RRHs a higher count of bifidobacteria was also found in the young subject compared with adults. Furthermore, the microbiota of RRHs showed qualitative differences. Indeed, Firmicutes was found to be the dominant phylum in Verona RRHs whereas Bacteroidetes was the most represented in Roma RRHs. At order level, Oscillospirales and Spirochaetales were the most represented in Verona RRHs compared with Rome RRHs, where Bacteroidales dominated over the other taxa. Finally, at the family level, RRHs from the two sites showed the presence of the same families, but with different levels of abundance. Our results highlight that the intestinal microbiota seems to reflect the lifestyle (i.e., the diet), whereas age and host genetics are the driving factors for the bifidobacterial population.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-10-25

Curated date: 2024/10/17

Curator: Prolific

Revision editor(s): Prolific, Aleru Divine, WikiWorks

Subjects

Location of subjects: Italy

Host species Species from which microbiome was sampled. Contact us to have more species added.: Potamochoerus porcus

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: Environmental factor environment factor,Environmental factor,environmental factor

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Potamochoerus porcus housed in Verona

Group 1 name Corresponds to the case (exposed) group for case-control studies: Potamochoerus porcus housed in Rome

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Potamochoerus porcus housed in Bioparco, Rome, Italy. This group included 2 adult individuals.

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: 2

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-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).: raw counts

Statistical test: DESeq2

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

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

Chao1 Abundance-based estimator of species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: decreased

Signature 1

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Curated date: 2024/10/17

Curator: Prolific

Revision editor(s): Prolific, Aleru Divine, WikiWorks

Source: Table 3 and Table S2

Description: Key microbial taxa that were differentially abundant in gut microbiota composition of Red River Hogs (Potamochoerus porcus) housed in Rome and Verona parks.

Abundance in Group 1: increased abundance in Potamochoerus porcus housed in Rome

NCBI	Quality Control	Links
Alloprevotella
Bacteroidota
Cellulosilyticum
Elusimicrobiota
Fibrobacterota
Lachnospira
Paludibacteraceae
Pseudomonadota
Sutterella
Sutterellaceae
Thermodesulfobacteriota
Thermoplasmatota
uncultured Eubacteriales bacterium
uncultured Lachnospiraceae bacterium
uncultured Prevotellaceae bacterium
Candidatus Paracaedibacteraceae

Revision editor(s): Prolific, Aleru Divine, WikiWorks

Signature 2

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Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/21

Curator: Prolific

Revision editor(s): Prolific, Aleru Divine, WikiWorks

Source: Table 3 and Table S2

Description: Key microbial taxa that were differentially abundant in gut microbiota composition of Red River Hogs (Potamochoerus porcus) housed in Rome and Verona parks.

Abundance in Group 1: decreased abundance in Potamochoerus porcus housed in Rome

NCBI	Quality Control	Links
Spirochaetaceae
Akkermansia
Defluviitaleaceae
unclassified Bacteroidales
Lactobacillaceae
Corynebacteriaceae
Treponema
Blautia
Candidatus Soleaferrea
unclassified Erysipelotrichaceae
Anaerostipes
Dorea
Papillibacter
unclassified Lachnospiraceae
Lactobacillus
unclassified Rikenellaceae
Corynebacterium
Bacillota
Spirochaetota
Verrucomicrobiota
Actinomycetota
Synergistota
Methanobacteriota
Planctomycetota
Patescibacteria group

Revision editor(s): Prolific, Aleru Divine, WikiWorks