Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk.

Human milk is the best nutrition for infants, providing optimal support for the developing immune system and gut microbiota. Hence, it has been used as source for probiotic strain isolation, including members of the genus Bifidobacterium, in an effort to provide beneficial effects to infants who cannot be exclusively breastfed. However, not all supplemented bifidobacteria can effectively colonise the infant gut, nor confer health benefits to the individual infant host; therefore, new isolates are needed to develop a range of dietary products for this specific age group.

Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.

Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements.

sp. nov., isolated from raw milk.

Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus but could not be assigned to any species with a validly published name. ATCC BAA-466 (97.

Simultaneous quantification of the most common and proteolytic Pseudomonas species in raw milk by multiplex qPCR.

The heat-stable peptidase AprX, secreted by psychrotolerant Pseudomonas species in raw milk, is a major cause of destabilization and premature spoilage of ultra-high temperature (UHT) milk and milk products. To enable rapid detection and quantification of seven frequent and proteolytic Pseudomonas species (P. proteolytica, P.

sp. nov., a novel proteolytic species isolated from cream.

During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106 and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status.

High counts of thermophilic spore formers in dairy powders originate from persisting strains in processing lines.

During the last decades, thermophilic spore counts became a very important quality parameter for manufacturers with regard to powdered dairy products. Low-spore count powders are highly demanded but challenging to produce when high production volume and long process times are intended. In this study a detailed monitoring of microbial levels in three skim milk powder plants was conducted.

gen. nov., sp. nov., a novel genus of the family isolated from bulk tank milk.

Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937, WS4759 and WS5303) constitute an independent phylogenetic lineage within the family with CCUG 36813 (93.7-94.

Genetic Organization of the Operon Affects the Proteolytic Potential of Species in Milk.

Psychrotolerant species are a main cause of proteolytic spoilage of ultra-high temperature (UHT) milk products due to the secretion of the heat-resistant metallopeptidase AprX, which is encoded by the first gene of the operon. While the proteolytic property has been characterized for many different isolates, the underlying gene organization was only described for a few strains so far. In this study, the phylogenomic analysis of 185 type strains revealed that the presence of is strongly associated to a monophylum composed of 81 species, of which 83% carried the locus.

Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.

Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of K12 grown in lysogeny broth medium and particularly focused on the size-selection step.

sp. nov., isolated from raw milk and skimmed milk concentrate.

Two strains, WS 5063 and WS 5067, isolated from raw cow's milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown, species by 16S rRNA and gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel species. It was most closely related to DSM 18928 with an ANIm of 91.

gen. nov., sp. nov., a novel bacterium of the family isolated from raw milk and dairy products and reclassification of as comb. nov.

Eight facultatively anaerobic rod-shaped bacteria were isolated from raw milk and two other dairy products. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates are placed in a distinct lineage within the family with and as the closest relatives (94.6 and 93.

sp. nov., isolated from raw milk and skimmed milk concentrate.

A polyphasic approach was used to investigate the taxonomic status of two bacterial strains, WS 5072 and WS 5092, isolated from skimmed milk concentrate and raw cow's milk. The 16S rRNA and gene sequences affiliated the strains to the same, hitherto unknown, species. Further examinations of the draft genomes based on multilocus sequence analysis and average nucleotide identity confirmed the presence of a novel species.

Proposal of Lysobacter pythonis sp. nov. isolated from royal pythons (Python regius).

The bacterial strains 4284/11T and 812/17 isolated from the respiratory tract of two royal pythons in 2011 and 2017, respectively were subjected to taxonomic characterization. The 16S rRNA gene sequences of the two strains were identical and showed highest sequence similarities to Lysobacter tolerans UM1 (97.2%) and Luteimonas aestuarii DSM 19680 (96.

Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of DSM 24698.

The aim of this study was to analyze the adaptation of the environmental DSM 24698 to anaerobiosis. The complete circular genome sequence of this species is reported and the adaptation of DSM 24698 to oxygen availability was investigated by global transcriptional analyses via RNAseq at 18 and 34°C. A list of operons was created based on the transcriptional data.

Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk.

Five strains, designated WS 4672T, WS 4998, WS 4992T, WS 4997 and WS 5000, isolated from bovine raw milk formed two individual groups in a phylogenetic analysis. The most similar species on the basis of 16S rRNA gene sequences were Pseudomonas azotoformans IAM 1603T, Pseudomonas gessardii CIP 105469T and Pseudomonas libanensis CIP 105460T showing 99.7-99.

Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86.

Lysinibacillus xylanilyticus belongs to the family Bacillaceae and was first described in 2010 with the type strain L. xylanilyticus XDB9. It is able to both degrade xylan and use it as the sole carbon source.

Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031.

Here, we report the draft genome sequence of Xanthomonas campestris LMG 8031, for which nearly no genetic information is available, despite its good xanthan-producing properties. We performed an Illumina-based sequencing approach of LMG 8031. The genome revealed a 5.

Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly.

Background: Next-generation sequencing (NGS) technology has paved the way for rapid and cost-efficient de novo sequencing of bacterial genomes. In particular, the introduction of PCR-free library preparation procedures (LPPs) lead to major improvements as PCR bias is largely reduced. However, in order to facilitate the assembly of Illumina paired-end sequence data and to enhance assembly performance, an increase of insert sizes to facilitate the repeat bridging and resolution capabilities of current state of the art assembly tools is needed.

Draft Genome Sequences of Three European Laboratory Derivatives from Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933, Including Two Plasmids.

Escherichia coliO157:H7 EDL933, isolated in 1982 in the United States, was the first enterohemorrhagicE. coli(EHEC) strain sequenced. Unfortunately, European labs can no longer receive the original strain.

Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe.

Background: Bacillus cereus sensu lato comprises eight closely related species including the human pathogens Bacillus anthracis and Bacillus cereus. Within B. cereus sensu lato, chromosomally and plasmid-encoded toxins exist.

Draft Genome Sequence of Bacillus cytotoxicus CVUAS 2833, a Very Close Relative to Type Strain NVH 391-98 Isolated from a Different Location.

We report the draft genome sequence of Bacillus cytotoxicus CVUAS 2833, isolated from potato puree in Germany (2007), which is-despite its clearly different source-very similar to the type strain B. cytotoxicus NVH 391-98 isolated in France (average nucleotide identity, 99.5%).

Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, Isolated from South Tyrolean Ham.

Staphylococcus carnosus is used as a starter culture in meat fermentation, where it contributes to color formation and produces aromatic compounds. Here, we report the first draft genome sequence of an S. carnosus subsp.