Dual pathogenicity island transfer by piggybacking lateral transduction.

Lateral transduction (LT) is the process by which temperate phages mobilize large sections of bacterial genomes. Despite its importance, LT has only been observed during prophage induction. Here, we report that superantigen-carrying staphylococcal pathogenicity islands (SaPIs) employ a related but more versatile and complex mechanism of gene transfer to drive chromosomal hypermobility while self-transferring with additional virulence genes from the host.

Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples.

Background: Novel strategies for anaerobic bacterial isolations from human faecal samples and various initiatives to generate culture collections of gut-derived bacteria have instigated considerable interest for the development of novel microbiota-based treatments. Early in the process of building a culture collection, optimal faecal sample preservation is essential to safeguard the viability of the broadest taxonomic diversity range possible. In contrast to the much more established faecal storage conditions for meta-omics applications, the impact of stool sample preservation conditions on bacterial growth recovery and isolation remains largely unexplored.

Variation and transmission of the human gut microbiota across multiple familial generations.

Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline.

Lateral transduction is inherent to the life cycle of the archetypical Salmonella phage P22.

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with early prophage excision followed by DNA replication and packaging (ERP). This temporal program is considered universal for P22-like temperate phages, though there is no direct evidence to support the timing and sequence of these events. Here we report that the long-standing ERP program is an observation of the experimentally favored Salmonella phage P22 tsc29 heat-inducible mutant, and that wild-type P22 actually follows the replication-packaging-excision (RPE) program.

sp. nov., a commensal spirochaete isolated from human faeces.

A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete (89.48 %).

Large-scale association analyses identify host factors influencing human gut microbiome composition.

To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10) threshold.

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses.

Recent population-based and clinical studies have identified a range of factors associated with human gut microbiome variation. Murine quantitative trait loci, human twin studies and microbiome genome-wide association studies have provided evidence for genetic contributions to microbiome composition. Despite this, there is still poor overlap in genetic association across human studies.

Metagenomic sequencing of clinical samples reveals a single widespread clone of responsible for porcine proliferative enteropathy.

is a Gram-negative obligate intracellular bacterium that is the aetiological agent of proliferative enteropathy (PE), a common intestinal disease of major economic importance in pigs and other animal species. To date, progress in understanding the biology of for improved disease control has been hampered by the inability to culture the organism . In particular, our understanding of the genomic diversity and population structure of clinical is very limited.

A multihost bacterial pathogen overcomes continuous population bottlenecks to adapt to new host species.

While many bacterial pathogens are restricted to single host species, some have the capacity to undergo host switches, leading to the emergence of new clones that are a threat to human and animal health. However, the bacterial traits that underpin a multihost ecology are not well understood. Following transmission to a new host, bacterial populations are influenced by powerful forces such as genetic drift that reduce the fixation rate of beneficial mutations, limiting the capacity for host adaptation.

Microbiota of human precolostrum and its potential role as a source of bacteria to the infant mouth.

Human milk represents a source of bacteria for the initial establishment of the oral (and gut) microbiomes in the breastfed infant, however, the origin of bacteria in human milk remains largely unknown. While some evidence points towards a possible endogenous enteromammary route, other authors have suggested that bacteria in human milk are contaminants from the skin or the breastfed infant mouth. In this work 16S rRNA sequencing and bacterial culturing and isolation was performed to analyze the microbiota on maternal precolostrum samples, collected from pregnant women before delivery, and on oral samples collected from the corresponding infants.

Genome hypermobility by lateral transduction.

Genetic transduction is a major evolutionary force that underlies bacterial adaptation. Here we report that the temperate bacteriophages of engage in a distinct form of transduction we term lateral transduction. Staphylococcal prophages do not follow the previously described excision-replication-packaging pathway but instead excise late in their lytic program.

Gene exchange drives the ecological success of a multi-host bacterial pathogen.

The capacity for some pathogens to jump into different host-species populations is a major threat to public health and food security. Staphylococcus aureus is a multi-host bacterial pathogen responsible for important human and livestock diseases. Here, using a population-genomic approach, we identify humans as a major hub for ancient and recent S.

Population Genomics of Legionella longbeachae and Hidden Complexities of Infection Source Attribution.

Legionella longbeachae is the primary cause of legionellosis in Australasia and Southeast Asia and an emerging pathogen in Europe and the United States; however, our understanding of the population diversity of L. longbeachae from patient and environmental sources is limited. We analyzed the genomes of 64 L.

Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?

Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as "obligate" or "facultative". Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life.

Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius.

Micromonospora strains have been isolated from diverse niches, including soil, water, and marine sediments and root nodules of diverse symbiotic plants. In this work, we report the genome sequence of Micromonospora lupini Lupac 08 isolated from root nodules of the wild legume Lupinus angustifolious.