Author's posts

Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii

A bacterial strain, designated J12C1-MA-4^(T), was isolated from liquid culture of the dinoflagellate Ceratoperidinium margalefii. The bacterium was Gram-negative, aerobic, and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at 30 °C, pH 7.0, in the presence of 1% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene and a 92 core gene set suggested that the strain J12C1-MA-4^(T) belongs to the family Rhodobacteraceae in the class Alphaproteobacteria and represents…

Novel Application of Survival Models for Predicting Microbial Community Transitions with Variable Selection for Environmental DNA

Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is underutilized in microbiome research to predict microbial community-mediated events, partly due to the sparsity and high-dimensional nature of the data. We advance the application of Cox proportional hazards (Cox PH) survival models to environmental DNA …

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Novel application of survival models for predicting microbial community transitions with variable selection for eDNA

Appl Environ Microbiol. 2022 Feb 9:AEM0214621. doi: 10.1128/AEM.02146-21. Online ahead of print. ABSTRACT Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is under-utilized in microbiome research to predict microbial community mediated events, partly due to the sparsity and high dimensional nature of the data. …

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Evolution of amino acid propensities under stability-mediated epistasis

Mol Biol Evol. 2022 Feb 4:msac030. doi: 10.1093/molbev/msac030. Online ahead of print. ABSTRACT Site-specific amino acid preferences are influenced by the genetic background of the protein. The preferences for resident amino acids are expected to, on average, increase over time because of replacements at other sites – a nonadaptive phenomenon referred to as the ‘evolutionary …

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Alexandriicola marinus gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from marine phycosphere

Two yellow-pigmented bacterial strains, LZ-14 ^(T) and ABI-LZ29, were isolated from the cultivable phycosphere microbiota of the highly toxic marine dinoflagellate Alexandrium catenella LZT09 and demonstrated obvious microalgae growth-promoting potentials toward the algal host. To elucidate the taxonomic status of the two bioactive bacterial strains, they were subjected to a polyphasic taxonomic characterization. Both strains were found to be Gram-negative, aerobic, rod-shaped and motile; to…

Alexandriicola marinus gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from marine phycosphere

Two yellow-pigmented bacterial strains, LZ-14 ^(T) and ABI-LZ29, were isolated from the cultivable phycosphere microbiota of the highly toxic marine dinoflagellate Alexandrium catenella LZT09 and demonstrated obvious microalgae growth-promoting potentials toward the algal host. To elucidate the taxonomic status of the two bioactive bacterial strains, they were subjected to a polyphasic taxonomic characterization. Both strains were found to be Gram-negative, aerobic, rod-shaped and motile; to…

Author Correction: Microbiome differential abundance methods produce different results across 38 datasets

Nat Commun. 2022 Feb 3;13(1):777. doi: 10.1038/s41467-022-28401-w. NO ABSTRACT PMID:35115546 | DOI:10.1038/s41467-022-28401-w

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of…

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of…

The Earth BioGenome Project 2020: Starting the clock

Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118. NO ABSTRACT PMID:35042800 | DOI:10.1073/pnas.2115635118