Draft genome of methanol-oxidizing Methylobacterium fujisawaense strain LAC1.

We report the draft genome of Methylobacterium fujisawaense LAC1 isolated from an acidic aquifer in Indian Head, MD, USA. The genome contains 5,883,000 bp and has a GC content of 70% with 5,434 protein-encoding genes with functional assignments. This strain can grow on methanol with lanthanum, a rare earth element.

Differential effects of the soluble fiber inulin in reducing adiposity and altering gut microbiome in aging mice.

Inulin, a soluble dietary fiber, is thought to exert multiple beneficiary effects through promoting growth of bacteria that metabolize the fiber to short-chain fatty acids (SCFAs); however, the effect and efficacy of inulin in aging subjects is unknown. This study aims to systematically evaluate the capacity of SCFAs production and host response in mice of different ages. Male C57BL/6J mice across young (5 months), middle (11 months) and old (26 months) age were subjected to a control diet for 2 weeks, followed by 6 weeks of inulin-containing diet. Inulin-induced increase in fecal butyric acid levels was most prominent in middle-age group compared to other age groups. In addition, inulin-induced increase in fecal propionic acids showed age-dependent decline. Interestingly, the SCFA-producing Roseburia was most abundantly and persistently increased in the middle-age group. Furthermore, inulin intake significantly reduced Firmicutes to Bacteroidetes ratio, and several dysbiotic bacteria associated with pro-inflammatory state. Concomitantly, circulating levels of CXCL1, a chemoattractant for neutrophils, was reduced by inulin intake. Inulin decreased fat mass in all age groups, with middle-aged mice being most responsive to fat-reducing effects of inulin. Moreover, inulin significantly increased energy expenditure and voluntary wheel running in middle-aged mice, but not in old mice. Overall, our data suggest that the efficacy of inulin in altering the microbiome and SCFA production, and the subsequent metabolic response was diminished in old mice, and highlight the importance of including age as a variable in studies determining host-microbe response to diets.

The Microbiota of Ixodes ricinus and Dermacentor reticulatus Ticks Collected from a Highly Populated City of Eastern Europe.

Recent investigations have examined, through sequencing the V6 region of 16S rRNA gene, the microbiota of questing Ixodes ricinus and Dermacentor reticulatus ticks collected from rural areas of Central (Dnipropetrovs'k (region D) and Poltava (region P)) and Northeastern (Kharkiv (region K)) Ukraine. In addition to defining the bacterial microbiota of both tick species, the previous investigations also revealed a high degree of inter-sex and inter-regional variations in the tick microbiota. As a continuation of the two studies, the present investigation has analyzed individual microbiota of questing I. ricinus (n = 50) and D. reticulatus (n = 50) ticks originating from Kyiv, the largest city of Ukraine. The Kyiv tick microbiota were compared between males and females for each tick species. Additionally, a cross-regional analysis was performed to compare the microbiota of Kyiv ticks to those from regions D, K, and P. Numerous statistically significant inter-sex and inter-regional variations were detected when alpha diversity, beta diversity, the bacterial relative and differential abundances were assessed. The overall results demonstrated that the microbiota of Kyiv ticks were statistically different compared to the ticks of the other three regions. Besides existing climatic and geographical differences between the four regions, the authors hypothesize that various anthropogenic factors of the megapolis (e.g., animal species translocation, land management, ecology) could have contributed to the distinct microbiota of Kyiv ticks observed in this study.

Identification of bacterial communities in extreme sites of Pakistan using high throughput barcoded amplicon sequencing.

Microorganisms thrive nearly everywhere including extreme environments where few other forms of life can exist. Geochemistry of extreme sites plays a major role in shaping these microbial communities and microbes thriving in such harsh conditions are untapped sources of novel biomolecules. To understand the structure and composition of such microbial communities, culture-independent bacterial diversity was characterised for two extreme sites in Pakistan, Khewra salt range and Murtazaabad hot spring. Barcoded amplicon sequencing technique was used to study the microbial communities. Physicochemical analysis of these sites was also conducted to study the dynamics of microbial communities under stressed conditions. Metagenomic sequencing of salt range soil samples yielded of 40,433 16S rRNA sequences, while hot spring sediments produced 76,449 16S rRNA sequence reads. Proteobacteria were predominant in saline soil while Firmicutes were most abundant in hot spring sediment. The taxonomic analysis of saline samples revealed 914 operational taxonomic units (OTUs) while that of hot spring sequences were clustered into 726 distinct OTUs. OTUs from genus Alkalibacillus were most abundant in hot spring sediments, whereas Haloarcula were more prevalent in saline soil. Some unidentified sequences were also present at each taxonomic level. Multivariate analysis indicated that electrical conductivity and pH are the major environmental factors involved in modelling microbial communities. This study revealed a poly-extremophilic microbial community in the Murtazaabad hot spring and characterised the unexplored halophilic microbial diversity of saline soil of Pakistan.

Extensive sex-specific and regional variations observed in the microbiome of Dermacentor reticulatus.

Recent progress in DNA sequencing technologies and advanced bioinformatic tools have enabled researchers to rapidly decipher the tick microbiome. To date, however, a number of microbiome studies performed on Dermacentor reticulatus ticks is still quite limited. Despite the importance of this ixodid tick for veterinary and human medicine, only two investigations have examined its microbiome. Moreover, these studies analyzed only a limited number of ticks/tick pools. Given the scarcity of microbiome data for D. reticulatus in general and the lack of microbiome studies on tick species from Eastern Europe in particular, the objective of the current investigation was to analyze the microbiome of D. reticulatus ticks collected from three geographical regions of Ukraine. A total of 88 individual tick microbiomes were analyzed by sequencing the V6 region of 16S rRNA. As a result, numerous significant differences in the bacterial relative abundance were detected between males and females of D. reticulatus for each region. The alpha diversity measures indicate that microbiomes were significantly different between females of D. reticulatus inter-regionally. In contrast, the collective results for male ticks are more suggestive of inter-regional microbiome homogeneity. The overall findings indicate that the composition and diversity of the D. reticulatus microbiome can be impacted by geographical and sex-related factors.

Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.

Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.

Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C.

Acidithiobacillus ferrooxidans, a chemolithoautotrophic bacterium, is well known for its mineral oxidizing properties. The current study combines experimental and whole genome sequencing approaches to investigate an iron oxidizing, extreme acidophilic bacterium, A. ferrooxidans isolate (IO-2C) from an acid seep area near Carlos, TX, USA. Strain IO-2C was capable of oxidizing iron i.e. iron sulphate and iron ammonium sulphate yielding shwertmannite and jarosite minerals. Further, the bacterium's genome was sequenced, assembled and annotated to study its general features, structure and functions. To determine genetic heterogeneity, it was compared with the genomes of other published A. ferrooxidans strains. Pan-genome analysis displayed low gene conservation and significant genetic diversity in A. ferrooxidans species comprising of 6926 protein coding sequences with 23.04% (1596) core genes, 46.13% (3195) unique and 30.82% (2135) accessory genes. Variant analysis showed >75,000 variants, 287 of them with a predicted high impact, in A. ferrooxidans IO-2C genome compared to the reference strain, resulting in abandonment of some important functional key genes. The genome contains numerous functional genes for iron and sulphur metabolism, nitrogen fixation, secondary metabolites, degradation of aromatic compounds, and multidrug and heavy metal resistance. This study demonstrated the bio-oxidation of iron by newly isolated A. ferrooxidans IO-2C under acidic conditions, which was further supported by genomic analysis. Genomic analysis of this strain provided valuable information about the complement of genes responsible for the utilization of iron and tolerance of other metals.

Natural selection interacts with recombination to shape the evolution of hybrid genomes.

To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the "minor" parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on swordtail hybrids stems predominantly from deleterious combinations of epistatically interacting alleles.

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS: We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS: Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION: We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.