Global distribution of mcr gene variants in 214,095 metagenomic samples

Since the initial discovery of a mobilized colistin resistance gene (mcr-1), several other variants have been reported, some of which might have circulated a while before being discovered. Metagenomic data provides an opportunity to re-analyze available older data to understand the evolutionary history of recently discovered antimicrobial resistance genes (ARGs). Here, we present a large-scale metagenomic study of 442 Tbp of sequencing reads from 214,095 samples to identify the host and geographical distribution and genomic context of nine mcr gene variants (mcr-1 to mcr-9). Our results show that the dissemination of each variant is not uniform. Instead, the source and location play a role in the spread. Despite the very diverse distribution, the genomic background of the mcr genes remains unchanged as the same mobile genetic elements and plasmid replicons occur. This work emphasizes the importance of sharing genomic data for surveillance of ARGs in our fight against antimicrobial resistance.

A Gastrointestinal Metagenomic Study On Mudskippers Supports Their Terrestrial Adaptation

-Purpose: The adaptability of blue-spotted mudskipper (Boleophthalmus Periophthalmodon; BP) and giant-fin mudskipper (Periophthalmus magnuspinnatus; PM), has been previously reported at the genome level to explain their amphibious life. However, the roles of GI microbiota in their adaptation to the terrestrial life are worth exploring. -Methods: In this study, we mainly utilized metagenomic data from these two representative mudskippers and typical aquicolous fish species to obtain microbial composition, diversity, abundance and potential functions of GI microbiota for comparisons between amphibious and aquicolous fishes. Meanwhile, we summarized the GI microbiota results of representative seawater fishes, freshwater fishes, amphibians, and terrestrial animals by literature mining for comparing those of the mudskippers. -Result: Interestingly the content for each dominant phylum was strikingly different among BP, PM and aquicolous fishes. We also observed that the profile of GI microbiota in mudskippers owned the typical bacterial families for the terrestrial animals, (freshwater and seawater) fishes, and amphibians at the same time, which is consistent with their life style of water-to-land and freshwater to seawater transition. More interestingly, certain bacteria strains like S24-7, previously thought to be specific in terrestrial animals, were also identified in both BP and PM. -Conclusion: The various composite and diversity of mudskipper GI microflora are therefore considered to conduce to their terrestrial adaptation in these amphibious fishes.

Metagenomic Study on Chinese Homemade Paocai: The Effects of Raw Materials and Fermentation Periods on the Microbial Ecology and Volatile Components

“Chinese paocai” is typically made by fermenting red radish or cabbage with aged brine (6–8 w/w). This study aimed to reveal the effects of paocai raw materials on fermentation microorganisms by metagenomics sequencing technology, and on volatile organic compounds (VOCs) by gas chromatography–mass spectroscopy, using red radish or cabbage fermented for six rounds with aged brine. The results showed that in the same fermentation period, the microbial diversity in cabbage was higher than that in red radish. Secundilactobacillus paracollinoides and Furfurilactobacillus siliginis were the characteristic bacteria in red radish paocai, whereas 15 species of characteristic microbes were found in cabbage. Thirteen kinds of VOCs were different between the two raw materials and the correlation between the microorganisms and VOCs showed that cabbage paocai had stronger correlations than radish paocai for the most significant relationship between 4-isopropylbenzyl alcohol, α-cadinol, terpinolene and isobutyl phenylacetate. The results of this study provide a theoretical basis for understanding the microbiota and their relation to the characteristic flavors of the fermented paocai.

Two Decades of Desiccation Biology: A Systematic Review of the Best Studied Angiosperm Resurrection Plants

Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models to understand the complex biology of vegetative desiccation tolerance. Despite extensive studies of resurrection plants, many details underlying the mechanisms of desiccation tolerance remain unexplored. To summarize the progress in resurrection plant research and identify unexplored questions, we conducted a systematic review of 15 model angiosperm resurrection plants. This systematic review provides an overview of publication trends on resurrection plants, the geographical distribution of species and studies, and the methodology used. Using the Preferred Reporting Items for Systematic reviews and Meta–Analyses protocol we surveyed all publications on resurrection plants from 2000 and 2020. This yielded 185 empirical articles that matched our selection criteria. The most investigated plants were Craterostigma plantagineum (17.5%), Haberlea rhodopensis (13.7%), Xerophyta viscosa (reclassified as X. schlechteri) (11.9%), Myrothamnus flabellifolia (8.5%), and Boea hygrometrica (8.1%), with all other species accounting for less than 8% of publications. The majority of studies have been conducted in South Africa, Bulgaria, Germany, and China, but there are contributions from across the globe. Most studies were led by researchers working within the native range of the focal species, but some international and collaborative studies were also identified. The number of annual publications fluctuated, with a large but temporary increase in 2008. Many studies have employed physiological and transcriptomic methodologies to investigate the leaves of resurrection plants, but there was a paucity of studies on roots and only one metagenomic study was recovered. Based on these findings we suggest that future research focuses on resurrection plant roots and microbiome interactions to explore microbial communities associated with these plants, and their role in vegetative desiccation tolerance.

Detection and Genomic Characterization of Senecavirus from Indian Pigs

Background: Senecavirus A (SVA), is a positive sense small non-enveloped RNA virus which belongs to Picornaviridae family and is responsible for porcine vesicular disease. The disease has been reported in many countries since late 2014, 2015 and 2016 like USA, Canada, Brazil, China and Thailand. Methods: In this study, the metagenomic study was performed on faecal samples of pigs/piglets suffering from diarrhea in Haryana, India with the help of next generation sequencing. The cDNA library was prepared from the faecal samples and run on the Illumina MiSeq instrument followed by identification and genomic characterization. Result: This study revealed the presence of SVA in the samples. The characterization of complete genome sequence of this strain showed complete nucleotide identity (100%) with SVA genomes reported from Canada, however, the polyprotein shares 98-99% amino acid sequence similarity with the genomes currently available in the GenBank. To the best of our knowledge this is the first report of SVA infection in pigs/piglets of Haryana, India. It demonstrates that an active and urgent surveillance of the swine population is required in the region. Additionally, the veterinarians must pay immediate attention to this vesicular disease and adopt preventive measures for its control.

Microorganisms of Two Thermal Pools on Kunashir Island, Russia

The Kuril Archipelago is a part of the Circum-Pacific Belt (Ring of Fire). These islands have numerous thermal springs. There are very few studies on these microbial communities, and none of them have been conducted by modern molecular biological methods. Here we performed the first metagenomic study on two thermophilic microbial communities of Kunashir Island. Faust Lake is hot (48 °C) and highly acidic (pH 2.0). We constructed 28 metagenome-assembled genomes as well as 17 16S ribosomal RNA sequences. We found that bottom sediments of Faust Lake are dominated by a single species of red algae belonging to the Cyanidiaceae family. Archaeans in Faust Lake are more diverse than bacteria but less abundant. The Tretyakovsky Thermal Spring is also hot (52 °C) but only weakly acidic (pH 6.0). It has much higher microbial diversity (233 metagenome-assembled genomes; 93 16S ribosomal RNAs) and is dominated by bacteria, with only several archaeans and one fungus. Despite their geographic proximity, these two thermal springs were found to not share any species. A comparison of these two lakes with other thermal springs of the Circum-Pacific Belt revealed that only a few members of the communities are shared among different locations.

BACTERIAL DIVERSITY WITH PLANT GROWTH-PROMOTING POTENTIAL ISOLATED FROM Agave americana RHIZOSPHERE

ABSTRACT Objective: Study the diversity of cultivable rhizospheric bacteria associated to Agave americana, and select native strains with potential as plant growth-promoting bacteria (PGPB). Design/methodology/approach: The isolated bacteria were phenotypically characterized. The genetic diversity and identity of the strains were revealed by genomic fingerprints and by sequencing of 16S rRNA gene. Plant growth promoting ability and plant inoculation assays were evaluated to know the potential as PGPB. Results: A total of 235 strains were isolated from A. americana rhizosphere and were classified within of 10 different bacterial genera. Rhizobium, Pseudomonas, Acinetobacter had high potential as PGPB. Study limitations/implications Cultivable approach was used to study rhizobacteria. A metagenomic study could expand the knowledge about the structure and diversity of bacterial community associated to A. americana. Findings/conclusions Rhizosphere bacteria have potential use as biofertilizer for the cultivation and propagation of A. americana and other agave species.