Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds

Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures

Microbiome differential abundance analysis methods for two groups are well-established in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as stages of a disease, and require different types of comparison. Standard pairwise comparisons are inefficient in terms of power and false discovery rates. In this Article, we propose a general framework, ANCOM-BC2, for performing a wide range of multigroup analyses with covariate adjustments and repeated measures. We illustrate our methodology through two real datasets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of patients with inflammatory bowel disease.

Actinobacteria From Desert: Diversity and Biotechnological Applications

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages

BACKGROUND

Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.).

RESULTS

A total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The "Candidatus Jiangella antarctica" has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa.

CONCLUSIONS

Our findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life. Video abstract.

Genome Sequences of Two Putative Streptogramin Producers, Streptomyces sp. Strains TÜ 2975 and TÜ 3180, from the Tübingen Strain Collection

Streptomyces sp. TÜ 2975 and TÜ 3180 are two strains from the Tübingen Actinomycetes strain collection. Here, we present the draft genome sequences of TÜ 2975 and TÜ 3180, with sizes of 7.62 Mb and 8.63 Mb, respectively.

Streptomyces sp. TÜ 2975 and TÜ 3180 are two strains from the Tübingen Actinomycetes strain collection. Here, we present the draft genome sequences of TÜ 2975 and TÜ 3180, with sizes of 7.62 Mb and 8.63 Mb, respectively.

Complete Genome Sequence of the Putative Phosphonate Producer Streptomyces sp. Strain I6, Isolated from Indonesian Mangrove Sediment

Streptomyces sp. strain I6 is a novel strain isolated from an Indonesian mangrove sediment sample. Bioinformatic analysis of the genome sequence of Streptomyces sp. I6 revealed 23 biosynthetic gene clusters. One of them encodes the synthesis of a putative phosphonate secondary metabolite, a class of underexplored natural compounds with great pharmaceutical potential.

Genome sequence and comparative analysis of Jiangella alba YIM 61503T isolated from a medicinal plant Maytenus austroyunnanensis

A draft genome sequence of Jiangella alba YIM 61503^T revealed a genome size of 7,664,864 bp arranged in 33 scaffolds. The genome was predicted to contain 7196 predicted genes, including 51 coding for RNA. Phylogenetic and comparative analyses of the draft genome of J. alba YIM 61503^T with the available genomes of other Jiangella species suggested a proximal similarity between strains J. alba YIM 61503^T and J. muralis DSM 45357^T, while indicating a high divergence between J. gansuensis YIM 002^T and other Jiangella species. The genome of J. alba YIM 61503^T also revealed genes involved in indole-3-acetic acid biosynthesis and an alkylresorcinols gene cluster. Further, detection of phosphotransferase genes in the genome of all Jiangella species indicated that they can uptake and phosphorylate sugars. The presences of TreX-Z, TreS and OtsA-OtsB genes in some of the Jiangella strains also indicated a possible mechanism for their tolerance of high salinity. Besides providing new insights into its genetic features, our results suggested that J. alba YIM 61503^T could be a potential strain for further genome mining studies. The release of this genome may, therefore, provide a better prospect for understanding "evolutionary taxonomy" about this genus in future.