Regulatory mechanism of cysteine-dependent methionine biosynthesis in : insights into sulfur metabolism in gut microbiota.

Sulfur, a critical element for bacterial growth, is not directly utilized by bifidobacteria, rendering the sulfur-containing amino acid biosynthesis pathway, particularly for cysteine and methionine, poorly understood. This research identifies six genes involved in this pathway through re-annotation of the DJO10A genome. These genes play crucial roles in bioconversion processes essential for cysteine utilization, highlighting its significance in sulfur metabolism.

Viability and Diversity of the Microbial Cultures Available in Retail Kombucha Beverages in the USA.

Kombucha is a two-stage fermented sweetened tea beverage that uses yeast and lactic acid bacteria (LAB) to convert sugars into ethanol and lactate and acetic acid bacteria (AAB) to oxidize ethanol to acetate. Its popularity as a beverage grew from claims of health benefits derived from this vibrant microbial bioconversion. While recent studies have shed light on the diversity of cultures in Kombucha fermentation, there is limited information on the diversity, and especially viability, of cultures in retail beverages that advertise the presence of Kombucha and probiotic cultures.

Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products.

The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju.

Development of an endolysin enzyme and its cell wall-binding domain protein and their applications for biocontrol and rapid detection of Clostridium perfringens in food.

Clostridium perfringens is a well-known pathogen that causes food-borne illnesses. Although bacteriophages can be effective natural food preservatives, phage endolysin and cell wall-binding domain (CBD) provide useful materials for lysis of C. perfringens and rapid detection.

Use of Lactococcus lactis as a production system for peptides and enzymes encoded by a Lantibiotic gene cluster from Bifidobacterium longum.

Bifidobacterium longum DJO10A was previously demonstrated to be able to produce a broad-spectrum lantibiotic, but production in media was very limited and only periodically on solid media. Given the difficulty of obtaining these lantibiotic peptides using B. longum DJO10A due to its tightly controlled production, genes predicted to be required for its production and immunity were designed and codon optimized according to the preferred codon used by Lactococcus lactis.

and the Pink Discoloration Defect in Cheese.

A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR).

Compromised Lactobacillus helveticus starter activity in the presence of facultative heterofermentative Lactobacillus casei DPC6987 results in atypical eye formation in Swiss-type cheese.

Nonstarter lactic acid bacteria are commonly implicated in undesirable gas formation in several varieties, including Cheddar, Dutch-, and Swiss-type cheeses, primarily due to their ability to ferment a wide variety of substrates. This effect can be magnified due to factors that detrimentally affect the composition or activity of starter bacteria, resulting in the presence of greater than normal amounts of fermentable carbohydrates and citrate. The objective of this study was to determine the potential for a facultatively heterofermentative Lactobacillus (Lactobacillus casei DPC6987) isolated from a cheese plant environment to promote gas defects in the event of compromised starter activity.

High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses.

Background: The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts.

Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese.

We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated.

Diabetes and renal disease: who does what?

Care of patients with diabetes and chronic kidney disease (CKD) in the UK is divided between primary care, diabetologists and nephrology. In a retrospective analysis, we examined the distribution of care provision for patients with diabetes and CKD. Nephrology services see a minority of diabetic patients with CKD, but they see the majority of those with an estimated glomerular filtration rate (eGFR) of <30 ml/min.

Nucleic acid-based approaches to investigate microbial-related cheese quality defects.

The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources.

Developing an efficient and reproducible conjugation-based gene transfer system for bifidobacteria.

Bifidobacteria are widely used as probiotics and have attracted increasing research interest worldwide. However, molecular techniques are still very scarce mainly due to the low efficiencies and strain-specific electroporation protocols that have been developed. Bacterial conjugation enables the transfer of genetic material among a relatively wide range of organisms and with virtually no size limitation.

Contribution of the Actinobacteria to the growing diversity of lantibiotics.

Currently, 76 lantibiotics have been described; the vast majority being produced by members of the Firmicute phylum of bacteria. There is a growing number being identified from the Actinobacteria phylum and some of these exhibit novel modifications leading to an increased functional diversity among lantibiotics. In this review, we discuss the currently characterized lantibiotics highlighting the expanding diversity provided by those from the Actinobacteria.

Effect of a synbiotic yogurt on levels of fecal bifidobacteria, clostridia, and enterobacteria.

While ingestion of synbiotic yogurts containing Bifidobacterium animalis subsp. lactis and inulin is increasing, their effect on certain microbial groups in the human intestine is unclear. To further investigate this, a large-scale, crossover-design, placebo-controlled study was utilized to evaluate the effect of a synbiotic yogurt containing B.

Transcription analysis of a lantibiotic gene cluster from Bifidobacterium longum DJO10A.

Bifidobacterium longum DJO10A was previously demonstrated to produce a lantibiotic, but only during growth on agar media. To evaluate the feasibility of production of this lantibiotic in broth media, a transcription analysis of the lanA gene was undertaken. Comparative microarray analysis of broth and agar cultures of B.

Constructivist learning of anatomy: gaining knowledge by creating anatomical casts.

Educators are encouraged to provide inquiry-based, collaborative, and problem solving activities that enhance learning and promote curiosity, skepticism, objectivity, and the use of scientific reasoning. Making anatomical casts or models by injecting solidifying substances into organs is an example of a constructivist activity for achieving these goals. This report describes a student-implemented protocol for making postmortem anatomical casts of the bronchial tree and coronary arteries of rats using Silastic® sealant.

Genomic insights into bifidobacteria.

Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford.

Genomics can advance the potential for probiotic cultures to improve liver and overall health.

The concept of probiotics has evolved immensely since it was first proposed a century ago. There are numerous potential health benefits attributed to certain probiotic bacteria, from preventing gastrointestinal (GI) infections to stimulating the immune system. Recent evidence is now quite compelling for a role of probiotics in enhancing liver health.

Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production.

Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol.

Comparative sequence analysis of plasmids from Lactobacillus delbrueckii and construction of a shuttle cloning vector.

While plasmids are very commonly associated with the majority of the lactic acid bacteria, they are only very rarely associated with Lactobacillus delbrueckii, with only four characterized to date. In this study, the complete sequence of a native plasmid, pDOJ1, from a strain of Lactobacillus delbrueckii subsp. bulgaricus was determined.

Identification of a nisI promoter within the nisABCTIP operon that may enable establishment of nisin immunity prior to induction of the operon via signal transduction.

Certain strains of Lactococcus lactis produce the broad-spectrum bacteriocin nisin, which belongs to the lantibiotic class of antimicrobial peptides. The genes encoding nisin are organized in three contiguous operons: nisABTCIP, encoding production and immunity (nisI); nisRK, encoding regulation; and nisFEG, also involved in immunity. Transcription of nisABTCIP and nisFEG requires autoinduction by external nisin via signal transducing by NisRK.

Involvement of the LlaKR2I methylase in expression of the AbiR bacteriophage defense system in Lactococcus lactis subsp. lactis biovar diacetylactis KR2.

The native lactococcal plasmid, pKR223, from Lactococcus lactis subsp. lactis biovar diacetylactis KR2 encodes two distinct bacteriophage-resistant mechanisms, the LlaKR2I restriction and modification (R/M) system and the abortive infection (Abi) mechanism, AbiR, that impedes bacteriophage DNA replication. This study completed the characterization of AbiR, revealing that it is the first Abi system to be encoded by three genes, abiRa, abiRb, and abiRc, arranged in an operon and that it requires the methylase gene from the LlaKR2I R/M system.

Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector.

Bifidobacterium longum DJO10A is a recent human isolate with probiotic characteristics and contains two plasmids, designated pDOJH10L and pDOJH10S. The complete sequences of both these plasmids have now been determined and consist of two circular DNA molecules of 10,073 and 3,661 bp, with G+C contents of 62.2% and 66.

Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis.

So far, there is only fragmentary and unconfirmed information on bacteriophages infecting the genus Bifidobacterium. In this report we analyzed three prophage-like elements that are present in the genomes of Bifidobacterium breve UCC 2003, Bifidobacterium longum NCC 2705, and Bifidobacterium longum DJO10A, designated Bbr-1, Bl-1, and Blj-1, respectively. These prophagelike elements exhibit homology with genes of double-stranded DNA bacteriophages spanning a broad phylogenetic range of host bacteria and are surprisingly closely related to bacteriophages infecting low-G+C bacteria.