New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300–500 mg L⁻¹ H₂S and <0.1 mg L⁻¹ O₂. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H₂S to H₂SO₄. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.

Tropical gar (Atractosteus tropicus), is freshwater and estuarine fish that has inhabited the Earth since the Mesozoic era, undergoing limited physiological variation ever since. This omnivorous fish is endemic to southern Mexico and part of Central America. Besides its recognized cultural and scientific relevance, the species has seen remarkable growth in its economic impact due to pisciculture. Previous studies have highlighted the role of microbial communities in fish, particularly those in the gut microbiome, in maintaining their host homeostasis or disease. In this study, we present the first report of the whole taxonomic composition of microbial communities in gut contents of adults’A. tropicus, by sex (female/male) and origin (wild/cultivated). Using culture-independent techniques, we extracted metagenomic DNA that was used for high throughput 16S rDNA profiling by amplifying the V4 – V5 hypervariable regions of the bacterial gene. A total of 364,735 total paired-end reads were obtained on an Illumina MiSeq sequencing platform, belonging to 508 identified genera, with the most and least abundant areCetobacterium, Edwardsiella, Serratia, Clostridium sensu stricto, PaludibacterandCampylobacter, Snodgrassella, Albirhodobacter, Lentilitoribacter, respectively. We detected that, by sex and origin, Proteobacteria, Fusobacteria, Firmicutes and Bacteroidetes phyla are the core gut microbiome of the adults’A. tropicus. We discover the Deinococcus-Thermus phylum sequence, wildtype males only, with extremophile capacity in another freshwater fish. We also identified the speciesLactococcus lactisstrains CAU929 and CAU6600, Cp6 and CAU9951,Cetobacteriumstrain H69,Aeromonas hydrophilastrains P5 and WR-5-3-2,Aeromonas sobriastrain CP DC28 andAeromonas hydrophilawith probiotic potential in aquaculture within the three dominant phyla, especially in wild-type organisms.