Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan

A total of 10 specimens were captured from selected sites of Bajaur Agency FATA, Pakistan using mist nets. The captured specimens were morphologically identified and various morphometric measurements were taken. The head and Body length (HB) of Pipistrellus coromondra and Pipistrellus kuhlii lepidus (n=10) was 43±0.11 mm and 45±1.1 respectively. Morphologically identified Pipistrellus kuhlii confirmed as Pipistrellus kuhlii lepidus based on 16S rRNA sequences. The DNA sequences were submitted to GenBank and accession numbers were obtained (MN 719478 and MT430902). The available 16S rRNA gene sequences of Pipistrellus coromondra and Pipistrellus kuhlii lepidus were retrieved from NCBI and incorporated in N-J tree analysis. Overall, the interspecific genetic variations among Pipistrellus coromondra and Pipistrellus kuhlii lepidus were 8% and 1% respectively. In our recommendation, a comprehensive molecular identification of bats is need of hour to report more cryptic and new species from Pakistan.

Genomic and Metabolic Features of an Unexpectedly Predominant, Thermophilic, Assistant Starter Microorganism, Thermus thermophilus, in Chinese Inner Mongolian Cheese

Inner Mongolian cheese is a traditional dairy product in China. It is produced without rennet, using naturally acidified milk that is simmered to achieve whey separation. In order to analyse the impact of simmering on the microbial community structure, high-throughput sequencing was performed to obtain bacterial 16S rRNA sequences from cheeses from the Ordos (ES), Ulanqab (WS), Horqin (KS) and Xilingol (XS) grasslands of Inner Mongolia. The relative abundance of an unexpected microorganism, Thermus thermophilus, ranged from 2% to 9%, which meant that its dominance was second only to that of lactic acid bacteria (LABs). Genome sequencing and fermentation validation were performed in T. thermophilus N-1 isolated from the Ordos, and it was determined that T. thermophilus N-1 could ingest and metabolise lactose in milk to produce lactate during the simmering process. T. thermophilus N-1 could also produce acetate, propionate, citrate and other organic acids through a unique acetate production pathway and a complete propionate production pathway and TCA cycle, which may affect texture and flavour development in Inner Mongolian cheese. Simultaneously, the large amount of citrate produced by T. thermophilus N-1 provides a necessary carbon source for continuous fermentation by LABs after the simmering step. Therefore, T. thermophilus N-1 contributes to cheese fermentation as a predominant, thermophilic, assistant starter microorganism unique to Chinese Inner Mongolian cheese.

ORPER: A Workflow for Constrained SSU rRNA Phylogenies

The continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER”, for “ORganism PlacER”, containerized in Singularity, which allows the determination the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

ORPER: a workflow for constrained SSU rRNA phylogenies

The continuous increase of sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects evermore complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow ORPER (containerized in Singularity), which allows determining the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

Molecular genetic diversity of some rabbit breeds based on mitochondrial 16S rRNA sequences

<p>The present study was performed to assess the genetic variations among six rabbit breeds in Egypt based on mitochondrial 16S rRNA sequences. The length of partial mitochondrial 16S rRNA in the six rabbit breeds ranged from 546 bp to 558 bp. The sequenced regions were submitted to GenBank/NCBI under accession numbers (MW052052 - MW052057). The average content of A+T was 57% in all breeds. Among breeds, the percentages of genetic distance values were ranged from 0.000 to 0.004. The highest P-distance (0.004) was found between the New Zealand White breed and all other breeds. The results support the suitability of mitochondrial 16S rRNA for genetic diversity analysis of rabbit breeds and the applicability for future research on genetic relationships and the phylogeny of rabbit breeds.</p>

Diversity In Intestinal Microorganisms Contributes To The Bodysize Difference In Chinese Horses And Ponies

Background: Intestinal microbiota communities can reflect the digestion and metabolism of the host, as well as the appearance of the host. In China, there are various excellent horse and pony breeds with rich diversity in wither height. However, little is known about the community structure of the intestinal microbiota in horses, let alone the profound effects it causes. Results: Here in, we generated 16S rRNA sequences of intestinal microorganisms from 118 Chinese horses including Guanzhong horse, Debao pony, and Ningqiang pony. We found that the intestinal microbiota of horses is full of diversity, and Firmicutes, Bacteroidetes, and Spirochaetes, which is consistent with the special structure of the horse digestive tract. Interestingly, the abundance of Firmicutes and Bacteroidetes at the phylum level, showed a strong correlation with horse height, with R values of 0.82 and -0.86 respectively. Moreover, at the genus level, Coprococcus, Streptococcus, Treponema, and Prevotella demonstrated higher significance in terms of height, the prediction of PICRUSt2 function and multiple analyses of the metabolic pathways, and additionally, the metabolic pathways of energy intake and utilization were significantly enriched in horses relative to ponies (P<0.01). Notably, flora colonization in mouse littermates contributed to their broad development compared to the control group. Conclusions: Compared with ponies, the intestinal microbiota enabled better cellulose decomposition and energy uptake in horses; Thus horses could get more energy from food to meet their higher demand for larger body development than ponies. Therefore, our study helps to understand the gut microbiota patterns across equine breeds, which has the potential to advance approaches aimed at personalized microbial modifications in horse breeding.

DNA barcoding of brackish and marine water fishes and shellfishes of Sundarbans, the world’s largest mangrove ecosystem

The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish, aquatic molluscs and crustaceans of Sundarbans mangrove wetland, to build a reference library of fish and shellfishes of this unique ecosystems. A total of 185 mitochondrial COI barcode sequences and 59 partial sequences of the 16S rRNA gene were obtained from 120 genera, 65 families and 21 orders of fish, crustaceans and molluscs. The collected samples were first identified by examining morphometric characteristics and then assessed by DNA barcoding. The COI and 16S rRNA sequences of fishes and crustaceans were clearly discriminated among genera in their phylogenies. The average Kimura two-parameter (K2P) distances of COI barcode sequences within species, genera, and families of fishes are 1.57±0.06%, 15.16±0.23%, and 17.79±0.02%, respectively, and for 16S rRNA sequences, these values are 1.74±.8%, 0.97±.8%, and 4.29±1.3%, respectively. The minimum and maximum K2P distance based divergences in COI sequences of fishes are 0.19% and 36.27%, respectively. In crustaceans, the K2P distances within genera, families, and orders are 1.4±0.03%, 17.73±0.15%, and 22.81±0.02%, respectively and the minimum and maximum divergences are 0.2% and 33.93%, respectively. Additionally, the present study resolves the misidentification of the mud crab species of the Sundarbans as Scylla olivacea which was previously stated as Scylla serrata. In case of molluscs, values of interspecific divergence ranges from 17.43% to 66.3% in the barcoded species. The present study describes the development of a molecular and morphometric cross-referenced inventory of fish and shellfish of the Sundarbans. This inventory will be useful in future biodiversity studies and in forming future conservation plan.

Ixodes tropicalis (Acari: Ixodidae) infesting a human and molecular detection of Rickettsia bellii, Colombia

Introduction: Ixodes tropicalis is a little-known tick species reported parasitizing wild rodents only in Colombia and Perú.Objective: To report a case of I. tropicalis infesting a human in the south of the metropolitan area of the Valle de Aburrá, Antioquia, Colombia, and to report the molecular detection of Rickettsia bellii in this species.Materials and methods: The tick was identified using a morphological key and sequencing of tick mitochondrial 16S rRNA. Additionally, bacterial and protozoa pathogens were evaluated using PCR for the detection of Rickettsia spp., family Anaplasmataceae, Borrelia spp., and piroplasmid.Results: We identified the tick as an I. tropicalis female according to Kohls, 1956, description and to partial 16S rRNA sequences showing a minimum of 5% divergencies compared to Ixodes sequences. We also detected the gltA gene of R. bellii in the tick with 99.87% of identity.Conclusion: This is the first report in Colombia of a species of the Ixodes genus parasitizing a human and the first report of the detection of R. bellii in this tick species.

First insights into molecular basis identification of 16 s ribosomal RNA gene of Staphylococcus aureus isolated from Sudan

Objective In this study, we analyzed the molecular evolution of Staphylococcus aureus isolates using 16S rRNA gene and phylogenetic analysis to detect the prevalence of S. aureus infections in Sudan. Results Molecular detection of S. aureus has shown that 20 (43.47%) of patients were positive for S. aureus. The phylogenetic tree of 16S rRNA sequences was divided into three lineages of S. aureus isolates detected from wound infections in Sudan. Nucleotides base-pair substitution was appeared at position 249. This mutation do not linked with Macrolides, Lincosamides and Streptogramines b resistant phenotype. Further studies should investigate the effect of that mutation on resistance to other antibiotics.