isolateR: an R package for generating microbial libraries from Sanger sequencing data.

Motivation: Sanger sequencing of taxonomic marker genes (e.g. 16S/18S/ITS/rpoB/cpn60) represents the leading method for identifying a wide range of microorganisms including bacteria, archaea, and fungi.

gen. nov., sp. nov., a member of a novel genus of the family , isolated from the gut of the western honey bee .

A Gram-negative, motile, rod-shaped bacterial strain, CA-0114, was isolated from the midgut of a western honey bee, . The isolate exhibited ≤96.43 % 16S rRNA gene sequence identity (1540 bp) to members of the families and .

Defined microbial communities and their soluble products protect mice from Clostridioides difficile infection.

Clostridioides difficile is the leading cause of antibiotic-associated infectious diarrhea. The development of C.difficile infection is tied to perturbations of the bacterial community in the gastrointestinal tract, called the gastrointestinal microbiota.

Metabolism of azo food dyes by bacterial members of the human gut microbiome.

Objectives: We set out to survey the capacities of bacterial isolates from the human gut microbiome to reduce common azo food dyes in vitro.

Methods: A total of 206 strains representative of 124 bacterial species and 6 phyla were screened in vitro using a simple azo dye decolorization assay. Strains which showed azoreductive activity were characterized by studies of azoreduction kinetics and bacterial growth.

gen. nov. sp. nov., isolated from a human clinical sample.

The diversity of bacteria associated with biopsy material obtained from patients with colorectal cancer was investigated using culture techniques. A novel bacterium, strain CC70A, was isolated by diluting a sample of homogenized tissue in anaerobic medium, and then plating to yield a pure culture. Strain CC70A was a Gram-positive, strictly anaerobic, motile, rod-shaped bacterium.

The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function.

The human colon is inhabited by a complex community of microbes. These microbes are integral to host health and physiology. Understanding how and when the microbiome causally influences host health will require microbiome models that can be tightly controlled and manipulated.

subgroup dominant microbiomes are associated with divergent cervicovaginal immune responses in a longitudinal cohort of Kenyan women.

Most cervicovaginal microbiome-immunology studies to date have relied on 16S rDNA microbial profiling which does not resolve the molecular subgroups of , believed to be central to the pathogenesis of bacterial vaginosis (BV) and subsequent risk of HIV acquisition. Here we used the 60 universal target which in addition to other microbial taxa, resolves four subgroups, for cervicovaginal microbial profiling in a longitudinal cohort of Kenyan women to examine associations with cellular and soluble markers of inflammation and HIV susceptibility. Participants (N = 41) were sampled, contributing 362 samples for microbiome analysis.

Metabolically-targeted dCas9 expression in bacteria.

The ability to restrict gene expression to a relevant bacterial species in a complex microbiome is an unsolved problem. In the context of the human microbiome, one desirable target metabolic activity are glucuronide-utilization enzymes (GUS) that are implicated in the toxic re-activation of glucuronidated compounds in the human gastrointestinal (GI) tract, including the chemotherapeutic drug irinotecan. Here, we take advantage of the variable distribution of GUS enzymes in bacteria as a means to distinguish between bacteria with GUS activity, and re-purpose the glucuronide-responsive GusR transcription factor as a biosensor to regulate dCas9 expression in response to glucuronide inducers.

Influence of free and immobilized chitosan on a defined human gut microbial ecosystem.

In this work, the influence of different forms of presentation of chitosan in the human gut microbiota with a defined bacterial community was evaluated. First, the susceptibility of individual gut bacterial isolates against chitosan was studied within a concentration range between 0.125 and 1 mg/mL.

Impact of food preservatives based on immobilized phenolic compounds on an in vitro model of human gut microbiota.

To address concerns about the biocompatibility of novel phenolic immobilization-based food preservatives, their impact on the composition and metabonomic profile of a defined community of human gut microbiota was evaluated. Three phenolics (eugenol, vanillin and ferulic acid) presented in two forms (free or immobilized on different supports) were tested at two concentration levels (0.5 and 2 mg/mL).

Culturing Human Gut Microbiomes in the Laboratory.

The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions.

A Generalist Lifestyle Allows Rare Gardnerella spp. to Persist at Low Levels in the Vaginal Microbiome.

Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C and D), and thirteen genome species have been defined recently.

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution.

Update on cpnDB: a reference database of chaperonin sequences.

cpnDB was established in 2004 to provide a manually curated database of type I (60 kDa chaperonin, CPN60, also known as GroEL or HSP60) and type II (CCT, TRiC, thermosome) chaperonin sequences and to support chaperonin sequence-based applications including microbial species identification, detection and quantification, phylogenetic investigations and microbial community profiling. Since its establishment, cpnDB has grown to over 25 000 sequence records including over 4 000 records from bacterial type strains. The updated cpnDB webpage (www.