by Hiroshi Nikaido — LB medium, also known incorrectly as Luria-Bertani medium, is widely used to grow bacterial cultures, mainly because it is easy to prepare and provides a broad base of nutrien…

RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...

In eukaryotes, ribosomal RNA genes (rDNA) encode the major ribosomal RNA molecules and are typically organized into a distinctive genomic structure involving tandem repetition of a polycistronic codin...

a blog for miscellaneous bioinformatics stuff

In desert ecosystems, microbial activity is driven by brief hydration pulses but is severely limited by persistent nutrient scarcity. Cyanobacteria...

Central conclusions rarely change when biomedical preprints go on to be published in journals.

Abstract. Cable bacteria are filamentous microbes that couple sulfide oxidation to oxygen reduction over centimeter distances via long-distance electron tr

Bi.po.la.ri.cau.lo'ta. N.L. masc. n. Bipolaricaulis, type genus of the phylum; -ota, ending to denote a phylum; N.L. neut. pl. n. Bipolaricaulota, the Bipolaricaulis phylum. Bipolaricaulota is a bact...

Some microbe species have evolved to stab, bomb, cannibalize, or poison each other. Can we harness their weapons for good?

Abstract. Microbial sulfur cycling is typically divided into an oxidative and a reductive branch, with microbes driving either sulfide oxidation or sulfate

Biological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.

The persistence of bacteria in various biofilms frequently leads to food spoilage and foodborne illnesses. Pseudomonas fluorescens is widely recognized as one of the most prevalent spoilage organisms,...

a blog for miscellaneous bioinformatics stuff

Contribute to treangenlab/emu development by creating an account on GitHub.

The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

Abstract. Microbial sulfur cycling is typically divided into an oxidative and a reductive branch, with microbes driving either sulfide oxidation or sulfate

Abstract. Microbial sulfur cycling is typically divided into an oxidative and a reductive branch, with microbes driving either sulfide oxidation or sulfate

Abstract. Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which

Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih

Nature Communications - Genome contamination may lead to an overestimation of horizontal gene transfer inferences

Comprehensive assessment of the host range of phages is a prerequisite for their safe and effective use in multiple applications but is rarely undertaken. This Review outlines the molecular and ecolog...

Abstract. When environmental bacteria transition to laboratory conditions, a process termed domestication, the shift from the native habitat to a culture m

The overwhelming majority of environmental microbes remain uncultured, limiting our understanding of their physiology and ecological roles. Although microbial interactions have been predicted as one o...

Chemically complex extracellular matrices define cellular microenvironments and shape cell behavior across all domains of life. But how has evoluti...

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

How complex multi-gene systems evolve across genetic backgrounds without disruptive epistasis remains unclear, particularly in highly exchangeable loci such as the capsule of Klebsiella pneumoniae. Th...

The development of an in silico typing database for Escherichia coli ABC transporter-dependent capsules enables analysis of capsule epidemiology and evolution for blood stream infection-associated E. ...

Nitrobacter species play a key role in nitrogen cycling; however, their physiological adaptations and genomic diversity remain largely underexplored. This study characterizes Nitrobacter vulgaris strain MLSD-S22, isolated from a nitrate- and heavy-metal-contaminated subsurface, revealing unexpected genomic and metabolic traits. Higher nitrite and oxygen affinities compared to previous reports indicate that some Nitrobacter are more competitive in low-substrate environments than previously believed. The presence of a complete nitrous oxide (N2O) reduction operon highlights the genomic potential related to N2O reduction within this genus; however, we did not observe N2O reduction under the conditions tested. By expanding Nitrobacter ecophysiology, this work provides a foundation for future research on the metabolic flexibility of Nitrobacter and their contributions to nitrogen transformations in diverse environments.