In the Life Sciences 'omics' data is increasingly generated by different high-throughput technologies. Often only integration of these allows uncovering biological insights that can be experimentally validated or mechanistically modelled, i.e. sophisticated computational approaches are required to extract complex non-linear trends present in omics data. Classification techniques allow training a model based on variables (e.g. SNPs genetic association studies) separate classes healthy...

Background Microorganisms in the human intestine (i.e. gut microbiome) have an increasingly recognized impact on health, including brain functioning. Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental associated with abnormalities dopamine neurotransmission and deficits reward processing its underlying neuro-circuitry ventral striatum. The microbiome might contribute to ADHD etiology via gut-brain axis. In this pilot study, we investigated potential differences between...

Significance Bacteria are constantly exposed to foreign elements, such as bacteriophages and plasmids. The CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR associated) adaptive immune systems provide heritable sequence-specific protection against these invaders. To develop immunity, bacteria add segments of nucleic acid their CRISPR memory. However, phage plasmid mutants can evade recognition by altering targeted sequence. responds evasion quickly generating...

Abstract Background Recent advances in sequencing technologies have enabled metagenomic analyses of many human body sites. Several studies catalogued the composition bacterial communities surface skin, mostly under static conditions healthy volunteers. Skin injury will disturb cutaneous homeostasis host tissue and its commensal microbiota, but dynamics this process not been studied before. Here we analyzed microbiota layer deeper layers stratum corneum normal investigated recolonization skin...

The ability of bacteria to adapt diverse environmental conditions is well-known. process bacterial adaptation a niche has been linked large changes in the genome content, showing that many genomes reflect constraints imposed by their habitat. However, some highly versatile are found habitats almost share nothing common. Lactobacillus plantarum lactic acid bacterium variety With aim unravelling link between evolution and ecological versatility L. plantarum, we analysed 54 strains isolated...

Lactococcus lactis is one of the most important micro-organisms in dairy industry for fermentation cheese and buttermilk. Besides conversion lactose to lactate it responsible product properties such as flavor texture, which are determined by volatile metabolites, proteolytic activity exopolysaccharide production. While species consists two subspecies cremoris their taxonomic position confused a group strains that, despite genotype, display phenotype. Here we compared analyzed (draft) genomes...

A common problem in the annotation of open reading frames (ORFs) is identification genes that are functionally similar but have limited or no sequence homology. This particularly case for bacteriocins, a very diverse group antimicrobial peptides produced by bacteria and usually encoded small, poorly conserved ORFs. ORFs surrounding bacteriocin often biosynthetic genes. information can be used to locate putative structural Here, we describe BAGEL, web server identifies DNA using novel,...

Many food fermentations are performed using mixed cultures of lactic acid bacteria. Interactions between strains key importance for the performance these fermentations. Yogurt fermentation by Streptococcus thermophilus and Lactobacillus bulgaricus (basonym, delbrueckii subsp. bulgaricus) is one best-described mixed-culture These species believed to stimulate each other's growth exchange metabolites such as folic carbon dioxide. Recently, postgenomic studies revealed that an upregulation...

Abstract Background Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge rate change over relevant timescales required. Methods We attempted estimate a molecular clock 199 isolates from epidemiologically linked cases, collected Netherlands spanning almost 16 years....

CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression several genes encoding proteins proteolytic system. DNA microarray analysis, comparing profiles L. and an isogenic strain in which codY was mutated, used to determine regulon. In peptide-rich medium exponentially growing cells, where exerts strong repressing activity, over 30 significantly increased upon removal codY. The differentially expressed included those predominantly involved amino acid...

The E-domain of cyclodextrin glycosyltransferase (CGTase) (EC 2.4.1.19) from <i>Bacillus circulans</i> strain 251 is a putative raw starch binding domain. Analysis the maltose-dependent CGTase crystal structure revealed that each enzyme molecule contained three maltose molecules, situated at contact points between protein molecules. Two these maltoses were bound to specific sites in E-domain, third was C-domain. To delineate roles and cyclization reaction kinetics two we replaced Trp-616...

High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site insertions by mutant-specific amplification sequence readout DNA flanking site, assigning measure essentiality based on number reads per insertion or gene. However, these large complex datasets hampered lack an easy...

There is growing interest in the beneficial effects of Lactobacillus plantarum on human health. The genome L. WCFS1, first sequenced 2001, was resequenced using Solexa technology. We identified 116 nucleotide corrections and improved function prediction for nearly 1,200 proteins, with a focus metabolic functions cell surface-associated proteins.

Background The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates survive a complex highly competitive ecosystem. Understanding how these communities function requires elucidating role of its key players, interactions among them with environment/host. Methods genome gut bacterium Romboutsia ilealis CRIB T was sequenced multiple technologies (Illumina paired-end, mate-pair PacBio). transcriptome HiSeq) after growth three different...

Gastrointestinal tumor growth is thought to be promoted by gastrointestinal bacteria and their inflammatory products. We observed that intestine-specific conditional Apc mutant mice (FabplCre;Apc15lox/+) developed many more colorectal tumors under conventional than pathogen-low housing conditions. Shotgun metagenomic sequencing plus quantitative PCR analysis of feces DNA revealed the presence two bacterial species in mice, absent from mice. One, Helicobacter typhlonius, has not been...

ABSTRACT Fructosyltransferase (FTF) enzymes produce fructose polymers (fructans) from sucrose. Here, we report the isolation and characterization of an FTF-encoding gene Lactobacillus reuteri strain 121. A C-terminally truncated version ftf was successfully expressed in Escherichia coli . When incubated with sucrose, purified recombinant FTF enzyme produced large amounts fructo-oligosaccharides (FOS) β-(2 → 1)-linked fructosyl units, plus a high-molecular-weight fructan polymer (&gt;10 7 )...

Several genes involved in nitrogen metabolism are known to contribute the virulence of pathogenic bacteria. Here, we studied function regulatory protein GlnR Gram-positive human pathogen Streptococcus pneumoniae. We demonstrate that mediates transcriptional repression glutamine synthesis and uptake (glnA glnPQ), glutamate (gdhA), gene encoding pentose phosphate pathway enzyme Zwf, which forms an operon with glnPQ. Moreover, expression gdhA is also repressed by pleiotropic regulator CodY. The...

Lactobacillus reuteri strain 121 employs a fructosyltransferase (FTF) to synthesize fructose polymer [a fructan of the levan type, with β(2→6) linkages] from sucrose or raffinose. Purification this FTF (a levansucrase), and identification peptide amino acid sequences, allowed isolation first levansucrase gene (lev), encoding protein (Lev) consisting 804 acids. Lev showed highest similarity an inulosucrase L. [Inu; producing inulin β(2→1)-linked fructosyl units] FTFs streptococci. Expression...

Nisin, a posttranslationally modified antimicrobial peptide produced by Lactococcus lactis, is widely used as food preservative. Yet, the mechanisms leading to development of nisin resistance in bacteria are poorly understood. We whole-genome DNA microarrays L. lactis IL1403 identify factors underlying acquired mechanisms. The transcriptomes and Nis(r), which reached 75-fold higher level, were compared. Differential expression was observed genes encoding proteins that involved cell wall...

ABSTRACT Lactococcus lactis is a lactic acid bacterium used in the production of many fermented dairy products. We report complete genome sequence L. subsp. KF147, nondairy strain isolated from mung bean sprouts. The circular chromosome 2,598,144 bp, largest among sequenced lactococcal strains, encodes properties related to adaptation plant environment.