The ggtree object is designed to store phylogenetic tree and associated data, and the object itself is a graphic object that can be rendered as an image file. This work will increase the reproducibility and reusability of phylogenetic data, as well as facilitate integrative and comparative studies.

Integrated Prokaryotes Genome and pan-genome Analysis (IPGA) serves as a free and easy-to-use web-based system that could provide up-to-date pan-genome analysis service for non-bioinformaticians. IPGA offers users the most reliable pan-genome profile which enables users to perform additional comparative genomic analysis. IPGA provides a series of downstream analysis modules such as phylogenetic inference, synteny inference, and target genome annotation.

TCM-Suite platform is composed of two sub-databases, Holmes-Suite and Watson-Suite. Holmes-Suite database covers six marker genes, resulting in 235,470 kinds of biological ingredients. Watson-Suite retrieved massive data for mining the “herb-compound-protein-disease” interpretation. A holistic pipeline was designed to connect Holmes and Watson, showed by a user-friendly platform.

TCM2COVID documents over 280 traditional Chinese medicine formulas (including over 300 herbs) with detailed clinical evidence and therapeutic mechanism information; TCM2COVID records over 80 natural products with detailed potential therapeutic mechanisms; TCM2COVID launches a useful web server for querying, analyzing, and visualizing documented formulas similar to those supplied by the user (formula similarity analysis).

This study presents the Microbial Biodegradation of Persistent Organic Pollutants Database (mibPOPdb) database, a web-accessible literature-based microbial biodegradation of persistent organic pollutants (POPs) resource. We also developed a robust chemical biodegradability prediction model with Graph Neural Networks. By providing high-level curated information on POP-degrading microbial communities, mibPOPdb will be an essential platform for fostering studies on microbial biodegradation of POP compounds and how these microbes would help solve the problem of POP accumulation. In addition, the in silico model can be used to evaluate the persistence of organic chemicals, which is a critical task in ecological risk assessment studies.

We developed a tool to get high-quality genomes with high taxonomic resolution by combining the cobarcoding information with public references. Compared with the conventional combination strategies, our pipeline generated a large number of high-quality genomes for the human microbial cobarcoding data sets.

The human-originated Lachnospiraceae biobank included 77 species was constructed. In vitro metabolite profiling of 110 Lachnospiraceae strains yielded 242 metabolites of 17 categories. Many Lachnospiraceae strains produce short-chain fatty acids, and Agathobacter rectalis strain Lach-101 and Coprococcus comes strain NSJ-173 are the top two butyric acid producers in vitro.

Multi-kingdom network construction increased network complexity. Multi-kingdom network construction increased negative edge proportion. Fungi stabilized multi-kingdom network structure. Fungi linked above- and below-ground biota at the community level.

The diversity, composition, and network of gut microbiota differed between the sympatric and diet-sharing Drosophila simulans and Dicranocephalus wallichii bowringi. Host species shape the bacterial and fungal community in two insect hosts by altering the relative contribution of community assembly processes. A minority of gut microbiota within D. simulans and D. wallichii bowringi are drawn from a regional microbial pool from waxberries, leaves, or soil. The composition of insect gut microbiota is driven by community assembly processes in a host species-dependent manner more than regional microbial pools.

In this study, we applied an algorithm to the keystone species identification in the gut microbiome, based on current causal inference theories and the dynamic intervention simulation. We identified the nonalcoholic steatohepatitis (NASH) keystone species combination, represented by Porphyromonas loveana, Alistipes indistinctus, and Dialister pneumosintes, that showed the highest potential for the microbial intervention of NASH.

The monosaccharide composition and glycosidic bond configuration determine the CAZyme that could hydrolyze it. Thus, bacteria encoding specific CAZyme utilize different structured dietary fibers. Compounded with bacterial interaction, gut microbiota dynamics is synergistically modulated.

We describe the biological and chemical components of the environmental exposomes in three major environmental matrices that are highly relevant to human and social-economical health—air, soil, and water. We discuss how different exposome components can interact with each other. Finally, we propose a list of outstanding challenges to be tackled to push the field forward.

Intestinal stem cells (ISCs) are protected by their niche and are regulated by Wnt, bone morphogenetic protein, and Notch. ISCs and their relationship with intestinal microbiota provide a feasible pathway to alleviate intestinal diseases. Diverse bacteria-related postbiotics regulate ISCs and maintain their homeostasis.

Advances in meta-omics provide a surge of marine RNA virus information. Deep marine virus discovery contributes greatly to the megataxonomy of RNA viruses. Understanding diversity and biogeography helps reveal the significance of marine RNA viruses, including evolutionary trajectories, hierarchical taxonomy, and ecological importance.

Eighteen novel RNA viruses were found in Crassostrea hongkongensis. Phylogenic analysis shows evidence of recombination between major genes of viruses. Picobirnaviruses are ubiquitous and abundant in oysters.

The pioneering plant Pueraria phaseoloides had a strong modulation effect on arbuscular mycorrhizal fungi (AMF) communities. Irrespective of geographical location, community composition of AMF in rhizosphere soil differed from that of the root. Co-occurrence network analysis revealed two AMF keystone species in rhizosphere soil (Acaulospora) and roots (Rhizophagus) of P. phaseoloides.

Donor participation is a critical part of ensuring the development of human microbiome research and the clinical application of fecal microbiota transplantation (FMT). Most FMT donors are still not sufficiently aware of the risks associated with the act of donating gut microbiota, especially the risk of data privacy disclosure. Enhanced awareness of the moral responsibility of the researchers and ethical oversight by ethics committees are needed.

We revealed abiotic components (extracellular polymeric substances, EPSs) in the periphytic biofilms. Further, the effect of the microbial community on the EPS, and the geodistribution patterns and ecological functions of the EPS were studied.

For the first time, updated molecular techniques were used to validate and elucidate the effect of the Panchagavya. Metagenomics was used to decipher the bacterial microbiome structure, which showed promising results for their existence and abundance in the Panchagavya.