Bifidobacteria and the infant gut: an example of co-evolution and natural selection.

Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut.

Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis.

Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels with their ratio being sensitive to the relative concentration ratio of dNTPs specified by the RNA template slippage-prone sequence and its 5' adjacent base. The GGG sequence 3' adjacent to the U6A shift/slippage site, which is important for ribosomal frameshifting, is shown here to limit reverse transcriptase base substitution and indel 'errors' in the run of A's in the product.

Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage.

RNA dependent DNA-polymerases, reverse transcriptases, are key enzymes for retroviruses and retroelements. Their fidelity, including indel generation, is significant for their use as reagents including for deep sequencing. Here, we report that certain RNA template structures and G-rich sequences, ahead of diverse reverse transcriptases can be strong stimulators for slippage at slippage-prone template motif sequence 3' of such 'slippage-stimulatory' structures.

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses.

Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host.

Global Survey and Genome Exploration of Bacteriophages Infecting the Lactic Acid Bacterium .

Despite the persistent and costly problem caused by (bacterio)phage predation of in dairy plants, DNA sequence information relating to these phages remains limited. Genome sequencing is necessary to better understand the diversity and proliferative strategies of virulent phages. In this report, whole genome sequences of 40 distinct bacteriophages infecting were analyzed for general characteristics, genomic structure and novel features.

Another Brick in the Wall: a Rhamnan Polysaccharide Trapped inside Peptidoglycan of .

Polysaccharides are ubiquitous components of the Gram-positive bacterial cell wall. In , a polysaccharide pellicle (PSP) forms a layer at the cell surface. The PSP structure varies among lactococcal strains; in MG1363, the PSP is composed of repeating hexasaccharide phosphate units.

Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses.

Functional constipation (FC) is a gastrointestinal disorder with a high prevalence among the general population. The precise causes of FC are still unknown and are most likely multifactorial. Growing evidence indicates that alterations of gut microbiota composition contribute to constipation symptoms.

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life.

Internally transcribed spacer (ITS) rRNA profiling is a novel tool for detailed analysis of microbial populations at low taxonomic ranks. Here we exploited this approach to explore species-level biogeography of the Bifidobacterium genus across 291 adult mammals. These include humans and 13 other primates, domesticated animals, such as dogs, cats, cows, sheep, goats, horses and pigs, and 46 additional species.

Host recognition by lactic acid bacterial phages.

Bacteriophage infection of lactic acid bacteria (LAB) is one of the most significant causes of inconsistencies in the manufacture of fermented foods, affecting production schedules and organoleptic properties of the final product. Consequently, LAB phages, and particularly those infecting Lactococcus lactis, have been the focus of intensive research efforts. During the past decade, multidisciplinary scientific approaches have uncovered molecular details on the exquisite process of how a lactococcal phage recognises and binds to its host.

Detecting Prophages by Mitomycin C-Mediated Induction Coupled to Flow Cytometry Analysis.

Most analyzed strains are predicted to harbor one or more prophage genomes within their chromosome; however, the true extent of the inducibility and functionality of such prophages cannot easily be deduced from sequence analysis alone. Chemical treatment of lysogenic strains with Mitomycin C is known to cause induction of temperate phages, though it is not always easy to clearly identify a lysogenic strain or to measure the number of released phage particles. Here, we report the application of flow cytometry as a reliable tool for the detection and enumeration of released lactococcal prophages using the green dye SYTO-9.

Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.

Background: Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic bacteria of the urogenital tract. The pan-genome of the genus Bifidobacterium has been explored in detail in recent years, though genomics of the Bifidobacteriaceae family has not yet received much attention. Here, a comparative genomic analyses of 67 Bifidobacteriaceae (sub) species including all currently recognized genera of this family, i.

The Sortase-Dependent Fimbriome of the Genus Bifidobacterium: Extracellular Structures with Potential To Modulate Microbe-Host Dialogue.

Bifidobacteria are important gut commensals of mammals, including humans, of any age. However, the molecular mechanisms by which these microorganisms establish themselves in the mammalian gut and persist in this environment are largely unknown. Here, we analyzed the genetic diversity of the predicted arsenal of sortase-dependent pili of known and sequenced members of the genus and constructed a bifidobacterial sortase-dependent fimbriome database.

Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures.

Despite being potentially highly useful for characterizing the biodiversity of phages, metagenomic studies are currently not available for dairy bacteriophages, partly due to the lack of a standard procedure for phage extraction. We optimized an extraction method that allows the removal of the bulk protein from whey and milk samples with losses of less than 50% of spiked phages. The protocol was applied to extract phages from whey in order to test the notion that members of 936 (now ), P335, c2 (now ) and phage groups are the most frequently encountered in the dairy environment.

The essential genomic landscape of the commensal Bifidobacterium breve UCC2003.

Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach.

Feeding the microbiota: transducer of nutrient signals for the host.

Advances in microbiome science cast light on traditional concepts on nutritional science, and are poised for clinical translation. Epidemiologic observations which linked lifestyle factors to risk of disease are being re-interpreted with mechanistic insight based on improved understanding of the microbiota. Examples include the role of dietary fibre in disease prevention, the deleterious effects of highly restricted diets, and the contribution of the microbiota to over- and undernutrition.

Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission.

Background: The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk.

Results: The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses.

Obesity and microbiota: an example of an intricate relationship.

It is widely accepted that metabolic disorders, such as obesity, are closely linked to lifestyle and diet. Recently, the central role played by the intestinal microbiota in human metabolism and in progression of metabolic disorders has become evident. In this context, animal studies and human trials have demonstrated that alterations of the intestinal microbiota towards enhanced energy harvest is a characteristic of the obese phenotype.

Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation.

Bacteria evolved over millennia in the presence of the vital micronutrient iron. Iron is involved in numerous processes within the cell and is essential for nearly all living organisms. The importance of iron to the survival of bacteria is obvious from the large variety of mechanisms by which iron may be acquired from the environment.

Genome Sequence of Phage BF.

Phages infecting , a common causative agent of nosocomial infections, have potential therapeutic applications. Here, we report the complete genome of the novel phage BF, representing the third-largest phage genome sequenced to date.

Next generation sequencing-based multigene panel for high throughput detection of food-borne pathogens.

Contamination of food by chemicals or pathogenic bacteria may cause particular illnesses that are linked to food consumption, commonly referred to as foodborne diseases. Bacteria are present in/on various foods products, such as fruits, vegetables and ready-to-eat products. Bacteria that cause foodborne diseases are known as foodborne pathogens (FBPs).

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches.

Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral 'dark matter' of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research.

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads.

No national legislation anywhere in the world regulates and protects traditional/typical sourdough breads. Sourdough fermentation is firmly associated with a century-old tradition, and with sensory and nutritional quality of breads. A well-defined cell density of lactic acid bacteria has to be reached at the end of fermentation, and be indirectly detectable in baked breads.

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.

Background: Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production.

Results: In the current study, we report on the complete sequencing of 16 L. lactis subsp.