These results suggested that housekeeping genes could be useful for H. pylori detection and to elucidate the mode of transmission and the relevance of the multiple infection.

Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France) were analyzed over 3 years during two different seasons (spring and autumn) and at different layers of the mat (0–2, 2–4, and 4–6 mm). To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i) inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii) a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%), followed by Archaea (∼4%) and Eukarya (∼1%). The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology) were significantly more abundant in the top layer (0–2 mm) than in the lower layers (2–4 and 4–6 mm). In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox reactions required for anaerobic respiration. Sulfatase genes had the highest relative abundance below 2 mm. Finally, chemotaxis signature genes peaked sharply at the oxic/photic and transitional oxic-anoxic boundary. This functional differentiation reflected the taxonomic diversity of the different layers of the mat.

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Aeromonas are autochthonous inhabitants of aquatic environments, including chlorinated and polluted waters, although they can also be isolated from a wide variety of environmental and clinical sources. They cause infections in vertebrates and invertebrates and are considered to be an emerging pathogen in humans, producing intestinal and extra-intestinal diseases. Most of the clinical isolates correspond to A. hydrophila, A. caviae, and A. veronii bv. Sobria, which are described as the causative agents of wound infections, septicaemia, and meningitis in immunocompromised people, and diarrhoea and dysenteric infections in the elderly and children. The pathogenic factors associated with Aeromonas are multifactorial and involve structural components, siderophores, quorum-sensing mechanisms, secretion systems, extracellular enzymes, and exotoxins. In this study, we analysed a representative number of clinical and environmental strains belonging to the A. hydrophila species complex to evaluate their potential pathogenicity. We thereby detected their enzymatic activities and antibiotic susceptibility pattern and the presence of virulence genes (aer, alt, ast, and ascV). The notably high prevalence of these virulence factors, even in environmental strains, indicated a potential pathogenic capacity. Additionally, we determined the adhesion capacity and cytopathic effects of this group of strains in Caco-2 cells. Most of the strains exhibited adherence and caused complete lysis.

Gut microbial structure in animals depends on the host, dietary habits and local environment. A random event, dietary change or antibiotic treatment may alter the gut environment with possible repercussions for the bacterial community composition and functionality and ultimately host fitness. The present study was focused on the composition, structure and functionality of gut microbiota in Reticulitermes grassei and the data obtained was compared with sequence surveys of three other Reticulitermes species. Each Reticulitermes species had a significantly different bacterial gut microbiota (pairwise significance tests using the Kolmogorov-Smirnov test), but a similar pattern of distribution (P-test in weighted Unifrac). The core gut microbiota from the analyzed Reticulitermes species contained 16 bacterial operational taxonomic units. Enzymes (KO) were detected from 14 pathways related to carbohydrate metabolism. R. grassei and R. hesperus, based on relative abundance of KO, had the most similar carbohydrate pathway patterns. In addition, we described the gut microbiota and functionality pathways in R. grassei after a 7-day dietary shift and antibiotic (ciprofloxacin) treatment. Both factors, but above all the antibiotic, altered the relative abundance of certain microbial groups, although the changes were not statistically significant (P-test in weighted Unifrac). The cellulose diet enhanced the carbohydrate pathways related to propanoate, butanoate, ascorbate, and glyoxylate metabolism. The antibiotic treatment affected galactose metabolism, the citrate cycle and inositol phosphate metabolism. Those functional changes may be related to changes in the abundance of several bacterial groups. Our findings provide insights into the stability of the gut microbiota in R. grassei and a resilience response to dietary shift or antibiotic treatment disturbance after 7 days.