Egyptian Mongoose (Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes

Abstract

The Egyptian mongoose (Herpestes ichneumon) is a medium-size carnivore that, in Europe, is restricted to Iberia. The bio-ecology of this species remains to be elucidated in several dimensions, including gut microbiota that is nowadays recognized as a fundamental component of mammals. In this work, we investigated the gut microbiota of this herpestid by single-molecule real-time sequencing of twenty paired male (n = 10) and female (n = 10) intestinal samples. This culture-independent approach enabled microbial profiling based on 16S rDNA and investigation of taxonomical and functional features. The core gut microbiome of the adult subpopulation was dominated by Firmicutes, Fusobacteria, Actinobacteria, and Proteobacteria. Eight genera were uniquely found in adults and five in non-adults. When comparing gut bacterial communities across sex, four genera were exclusive of females and six uniquely found in males. Despite these compositional distinctions, alpha- and beta-diversity analyses showed no statistically significant differences across sex or between adult and non-adult specimens. However, when function was inferred, males presented a significantly higher abundance of amino acid and citrate cycle metabolic pathways, compared to the significant overrepresentation in females of galactose metabolic pathways. Additionally, adults exhibited a significantly higher abundance of cationic antimicrobial peptide resistance pathways, while non-adults bared a significant overrepresentation of two-component systems associated with antibiotic synthesis, flagellin and biofilm production, and chemotaxis control. This study adds new insights into the mongoose bio-ecology palette, highlighting taxonomical and functional microbiome dissimilarities across sex and age classes, possibly related to primary production resources and life-history traits that impact on behavior and diet.

Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome

“…Sample storage, enrichment, pasteurization, and inoculation were performed as described elsewhere [25]. The fecal samples (2.5 g) were homogenized and divided into two parts, 0.5 g were used in the previous microbial profiling work [10] and 2 g were used in this study. The samples (2 g) were divided into two equal parts, homogenized in buffered peptone water (10 mL), and incubated at 37 • C for 24 h under aerobic (with O2) and anaerobic (without O2) conditions.…”

“…The culturomics data acquired in this study was compared with the data obtained from the same specimens by a microbial profiling approach [10]. Microbial profiling was performed as described elsewhere [10].…”

“…The culturomics data acquired in this study was compared with the data obtained from the same specimens by a microbial profiling approach [10]. Microbial profiling was performed as described elsewhere [10]. Briefly, the DNA was extracted from 500 mg of feces of each mongoose using the NZYSoil gDNA isolation kit (NZYTech, Lisbon, Portugal), followed by the amplification of the full-length 16S rRNA gene, and subsequently, the amplicons were sequenced on the PacBio SMRT RS-II platform (Pacific Biosciences, Menlo Park, CA, USA; commercially available at Eurofins Genomics, München, Germany).…”

“…In previous work, we investigated the gut microbiota of the Egyptian mongoose (Herpestes ichneumon, Linnaeus, 1758), a medium-sized mammalian carnivore from the Herpestidae family, by applying microbial profiling to the 16S rRNA gene sequences of twenty paired male (n = 10) and female (n = 10) intestinal samples [10]. The core gastrointestinal microbiota of this population was dominated by Firmicutes (86%), Actinobacteria (6%), Fusobacteria (3%), Proteobacteria (3%), and Bacteroidetes (1%), with Clostridioides (25%) and Clostridium (19%) being the most abundant genera.…”

“…Comparison of the intestinal bacterial microbiota of the Egyptian mongoose between culturomics and microbial profiling[10] approaches. (A) Relative abundance at a phylum level; (B) Relative abundance at the genus level.…”