Hi-C deconvolution of a textile dye-related microbiome reveals novel taxonomic landscapes and links phenotypic potential to individual genomes

Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider

Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.

Dye degradation by early colonizing marine bacteria from the Arabian Sea, India

Malachite green dye belongs to the triphenylmethane group and is a common environmental pollutant that threatens non-target organisms. We report the potential of the early colonizing marine bacterium Pseudomonas sp. ESPS40 isolated from the Arabian Sea, India, to decolorize malachite green (MG). The bacterium ESPS40 exhibited a higher ability for MG degradation (86-88%) at varying NaCl concentrations (1-3%). The highest MG degradation (~ 88%) was observed at 1% NaCl. The bacterial strain ESPS40 showed degradation up to 800 mg L^-1 MG. Further, enzyme activities such as tyrosinase (63.48-526.52 U L^-1) and laccase (3.62-28.20 U L^-1) were also analyzed with varying concentrations (100 mg L^-1-1000 mg L^-1) of MG during the degradation process. The dye degradation was confirmed by Fourier transform infrared spectroscopy (FTIR) and high-performance liquid chromatography (HPLC). The outcome of the present study demonstrated Pseudomonas sp. ESPS40 as a potential strain for the efficient degradation of MG at higher concentrations. Thus, Pseudomonas sp. ESPS40 can be utilized as a potential candidate for the biodegradation of MG in wastewater treatment.

Draft Genome Sequence of Methanobacterium paludis IBT-C12, Recovered from Sediments of the Apatlaco River, Mexico

Methanobacterium paludis is a hydrogenotrophic archaea first described in 2014 and isolated from a peatland area. So far, there is only one sequenced genome of this taxon. Here, we report the draft genome sequence of M. paludis IBT-C12, a metagenome-assembled genome (MAG) from sediments in the Apatlaco River, Mexico.

Enrofloxacin Alters Fecal Microbiota and Resistome Irrespective of Its Dose in Calves

Enrofloxacin is a fluoroquinolone drug used to prevent and control bovine respiratory disease (BRD) complex in multiple or single doses, ranging from 7.5 to 12.5 mg/kg body weight. Here, we examined the effects of high and low doses of a single subcutaneously injected enrofloxacin on gut microbiota and resistome in calves. Thirty-five calves sourced for this study were divided into five groups: control (n = 7), two low dose groups (n = 14, 7.5 mg/kg), and two high dose groups (n = 14, 12.5 mg/kg). One group in the low and high dose groups was challenged with Mannheimia haemolytica to induce BRD. Both alpha and beta diversities were significantly different between pre- and post-treatment microbial communities (q < 0.05). The high dose caused a shift in a larger number of genera than the low dose. Using metagenomic ProxiMeta Hi-C, 32 unique antimicrobial resistance genes (ARGs) conferring resistance to six antibiotic classes were detected with their reservoirs, and the high dose favored clonal expansion of ARG-carrying bacterial hosts. In conclusion, enrofloxacin treatment can alter fecal microbiota and resistome irrespective of its dose. Hi-C sequencing provides significant benefits for unlocking new insights into the ARG ecology of complex samples; however, limitations in sample size and sequencing depth suggest that further work is required to validate the findings.