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Breast and ovarian cancers are the most common cancer types in females worldwide and in India. Patients with these cancers require an early diagnosis which is essential for better prognosis, treatment and improved patient survival. Recently, the utilization of next-generation sequencing (NGS)-based screening has accelerated molecular diagnosis of various cancers. In the present study, we performed whole-exome sequencing (WES) of 30 patients who had a first or second-degree relative with breast or ovarian cancer and are tested negative for BRCA1/2 or other high and moderate-risk genes reported for HBOC. WES data from patients were analyzed and variants were called using bcftools. Functional annotation of variants and variant prioritization was performed by Exomiser. The clinical significance of variants was determined as per ACMG classification using Varsome tool. The functional analysis of genes was determined by STRING analysis and disease association was determined by open target tool. We found novel variants and gene candidates having significant association with HBOC conditions. The genes identified by exomiser (phenotype score 0.75) are associated with various biological processes such as DNA integrity maintenance, transcription regulation, cell cycle regulation, and apoptosis. Our findings provide novel and prevalent gene variants associated with the HBOC condition in the West Indian population which could be further studied for early diagnosis and better prognosis of HBOC.

The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.

Background COVID-19 pandemic has shaken the entire world and the socio-economic life on the planet. The implications of the bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations among the COVID-19. Identification and association of the nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal microbiota dynamics that may determine and/or influence the disease outcome in the COVID-19 patients. Results Here, in this study, we present distinct nasopharyngeal microbiome in the demised (N=48) and recovered (N=29) COVID-19 patients as compared to the control group (N=33). The nasal microbiome composition in the three groups vary significantly (PERMANOVA, p-value orynebacterium (LAD score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were found as biomarkers (p-value Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), the recovered group harbors ordinal bacteria (p-value Pseudomonas (LDA score 6.19), and several healthy oral/nasal cavity commensal including Veillonella, and Porphyroonas, were biomarkers for the control individuals. Conclusions Dysbiosis in the commensal nasopharyngeal microbiota, especially due to infection of opportunistic pathogens could lead to more complex and severe COVID-19 disease dynamics. Whereas, healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may help in preventing the viral infection and possible recovery which is yet to be explored. The findings in the present study provide key considerations and have significant implications for the COVID-19 treatment and control measures. However, further study is required to address the microbiome based therapeutic aspects.

Background Breast and ovarian cancers are the most common cancer types in females in India which pertain to higher mortality and morbidity due to late diagnosis and poor prognosis. Early diagnosis for better prognosis improve the patient’s treatment and survival. The next-generation sequencing (NGS)-based screening has accelerated molecular diagnosis of various cancers. Methods We performed whole exome sequencing (WES) of 30 patients who had a first or second degree relative with breast or ovarian cancer. Further, all these patients are tested negative for BRCA1/2 or other high and moderate risk genes reported for HBOC. WES data from 30 patients were analyzed and variants were called using bcftools. Functional annotation of variants and variant prioritization was performed by Exomiser. The clinical significance of variants was determined by Varsome tool. The functional analysis of genes was determined by STRING analysis and disease association was determined by open target tool. Results We examined the variants based on the prevalence of variants among 30 patients i.e. frequency and disease association determined by the phenotype score of exomiser. From both the approaches, we found novel variants and novel gene candidates associated with HBOC conditions. The variants in HYDIN, AVIL, IWS1, PLA2G6, PRDM4, ST3GAL2, and ZNF717 were predicted highly oncogenic. Moreover, we also found 59 genes having higher phenotype score (phenotype score >0.75) and which are associated with various biological processes such as DNA integrity maintenance, transcriptional regulation, cell cycle and apoptosis. Conclusion The gene variants associated with HBOC condition in West Indian cohort have been revisited. Our findings provide novel as well as highly prevalent variants in the population which could be further studied in detail for their use in early diagnosis and better prognosis of HBOC patients.

Textile industries play an important role in uplifting the national economies worldwide. Nevertheless, they generate a huge amount of intensive colored effluent, which is a serious threat to the environment. The microbial communities present in these highly polluted environmental sites help in remediating pollutants naturally. However, little is known about their genes and enzymes in the textile wastewater systems. In this study, we explored the microbial community structure and their functional capability in three different wastewater systems, i.e., industry sites, effluent treatment plant (ETP), and common effluent treatment plant (CETP). Our findings based on shotgun metagenomics highlight the varied bacterial diversity at the three industry sites. Overall, the major dominant phyla in the industry site and CETP samples were Proteobacteria and Bacteroidetes, while in the ETP site, Firmicutes, Cyanobacteria, and Proteobacteria were predominant. The final discharge sample site was having a higher proportion of the Proteobacteria and Bacteroidetes. Aeromonas caviae, Desulfovibrio desulfuricans, Klebsiella pneumoniae, Pseudomonas stutzeri, Shewanella decolorationis, Shewanella oneidensis, Shewanella putrefaciens, and Vibrio cholera were the abundant species across the three sites. Furthermore, this research study identified the key microbial genes encoding enzymes having a known role in textile dye and aromatic compound degradation. Functional annotation of the shotgun metagenome samples indicates the presence of reductase, azoreductase, nitrate/nitrite reductase, and oxidoreductase enzyme encoding genes. Our findings provide the shotgun metagenomics-based approach for mining the textile dye degrading genes and genomic insights into the bioremediation of textile industrial effluent.

Genomic surveillance of SARS-CoV-2 has played a decisive role in understanding the transmission and evolution of the virus during its emergence and continued circulation. However, limited genomic sampling in many high-incidence countries has impeded detailed studies of SARS-CoV-2 genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. To address this gap, we investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during its first epidemic wave and shed light on virus’ spread in one of the pandemic’s hardest-hit regions. By integrating regional case data and 434 whole virus genome sequences sampled across 20 districts from March to July 2020, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat, India. Our findings revealed that global and regional connectivity, along with population density, were significant drivers of the Gujarat SARS-CoV-2 outbreak. The three most populous districts in Gujarat accounted ∼84% of total cases during the first wave. Moreover, we detected over 100 virus lineage introductions, which were primarily associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations with low-population density. Our findings suggest SARS-CoV-2 transmission follows a gravity model in India, with urban centres contributing disproportionately to onward virus spread.

The rhizosphere, a narrow zone of soil near plant roots, is a hot spot for microbial activity. Rhizosphere microbiota directly or indirectly benefit plants by supplementing nutrients, producing beneficial chemicals, or suppressing pathogens. Plants attract and modulate bacteria within the rhizosphere by releasing exudates. Plants also tend to select the rhizosphere microbiota based on their needs; a phenomenon termed as “rhizosphere effect”. In this study, we characterized the rhizosphere microbiota of peanut plants across the crop development cycle from pre-sowing of seeds to post-harvest of crop under field conditions. The rhizosphere and bulk soil samples from different crop developmental stages were also compared. The composition of bulk soil microbiota resembled microbiota of pre-sowing and post-harvest soil and was markedly different from rhizosphere soil samples. Rhizosphere samples were enriched with multiple organisms mostly from the Proteobacteria, Firmicutes and Bacteroidota phyla. Differences in diversity were observed among the rhizosphere samples but not in bulk soil across different crop development stages. Pseudomonas_M indica was highly enriched during the germination of seeds. Furthermore, Plant Growth Promoting (PGP) bacteria like Bacillus were enriched during the middle stages of crop development but there was a decline in PGP organisms in the matured crop stage. We also observed a significant association of pH and Electrical Conductivity (EC) with the profiles of microbial community. Overall, this study portrayed the changes in rhizosphere microbiota of peanut during different developmental stages of crop and may help to design stage specific bio-strategies such as bio-fertilizer to improve crop yield.

Background: Implantation failure limits the success rate of natural and in vitro fertilization (IVF)-assisted conceptions. Evidence suggests dysbiosis in the female reproductive tract impacts implantation failure. However, whether gut dysbiosis influences implantation failure and whether it accompanies reproductive tract dysbiosis remains unexplored.Method: We recruited 11fertile women as the controls, and a cohort of 20 women diagnosed with implantation-failure associated infertility, which included 10 women diagnosed with recurrent implantation failure (RIF), and 10 women diagnosed with unexplained infertility (UE). Using next-generation amplicon sequencing, we compared the diversity, structure, and composition of fecal and vaginal bacteria of the controls with that of the infertile cohort. While we sequenced fecal samples of all the participants (n=31), we could only sequence 8 vaginal samples in each group (n=24).Results: Compared with the controls, α-diversity of the gut bacteria, analysed by Chao 1 and Shannon indices, among the infertile groups declined (p p Firmicutes, in the RIF group. In contrast, Gram-negative bacteria were relatively more abundant in the UE group. Additionally, mucus-producing bacteria genera such as Prevotella and Sutterella declined in the infertile cohort (p p Hungatella, associated with trimethylamine N-oxide (TMAO) production, occurred in the infertile cohort. Vaginal microbiota was dominated by L. iners across the groups, with the UE group showing the highest levels. Of the three groups, the RIF group had the least diverse vaginal microbiota. Taxa analysis showed higher levels of anaerobic bacteria such as Leptotrichia, Snethia , and Prevotella in the controls.Conclusion: We posit that in the setting of the compromised gut mucosal barrier, the phyla Firmicutes generates TNF-α - driven systemic inflammation, leading to RIF, whereas an overload of Gram-negative bacteria induces IL-6-driven systemic inflammation, leading to UE. Additionally, Hungatella-induced elevation of TMAO levels causes platelet hypercoagulability, synergistically contributing to implantation failure. Finally, vaginal dysbiosis does not appear to co-occur with gut dysbiosis.

Contrary to the conventional genomic surveillance based on clinical samples (symptomatic patients), the wastewater-based genomic surveillance can identify all the variants shed by the infected individuals in the population, as it does also include RNA fragmented shredded by clinically escaped asymptomatic patients. We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/ Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis showed a total of 35 mutations in the spike protein across four samples categorized into 23 types. We noticed the presence of spike protein mutations linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not observed in the samples of Sep and Nov 2020 but appeared before the devastating second wave of COVID-19, which started in early April 2021 in India, caused rapid transmission and deaths all over India. We found the genetic traces of the B.1.617.2 in samples of early Feb 2021 i.e., more than a month before the first clinically confirmed case of the same variant in March 2021 in Ahmedabad, Gujarat. The present study tells about the circulating variants in Ahmedabad and suggests early prediction VOCs employing the wastewater genomic surveillance approach that must be exploited at a large scale for effective COVID-19 management.HighlightsWhole-genome sequencing of SARS-CoV-2 from the WW samples was carried out.Variant of Concern (VoC: VOC-21APR-02; B.1.617.2) were detected in WW samples.WBE may detect prevalent SARS-CoV-2 variants and monitor their cryptic transmissionWW genomic surveillance can aid the decision-making system for public health policies.

In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.

Background: Different human populations across the globe responded in a different way against the SARS-CoV-2 infection. Therefore, it is anticipated that host genetic variants have straight association with the COVID-19. Genome Wide Association Study (GWAS) may help to understand this aspect. Methods: We carried out GWAS analysis with 571 SARS-CoV-2 infected patients from Gujarat state of India with different phases of COVID-19 severity. After quality filtering, total 94, 320 and 147, deceased, recovered (after admitting in intensive care unit), and asymptomatic, patients were included in the final analysis using three tools i.e. PLINK, OrdinalGWAS·jl and SAIGE. Findings: We identified total ten, thirteen, and ten unique genomic loci for deceased vs recovered, deceased vs asymptomatic and recovered vs asymptomatic groups, respectively. TNFSF4, LRRC56 and TUBD1 genes have shown an association in deceased vs recovered. Similarly, genomic markers where nearby genes are OR7C2, OR7A17, PAX5, etc. are significant for disease vs asymptomatic comparison. For recovered vs asymptomatic comparison, a strong signal at chromosome 6, locus 6p21·32 where HLA group of genes, which are key regulators of the immune system, is found. Unfavorable alleles in AX-11318356, AX-11403743, and AX-11509434 have shown the higher frequency in European compared to the South Asian population and it is reversed for AX-40266551, AX-40266553, AX-38975337, AX-11258333, and AX-30353919. Interpretation: Unfavorable alleles of the markers showing association with the disease severity and outcome can be used for risk prediction in the SARS-CoV-2 infections. GWAS study in other populations may help to further strengthen the outcome of this study. Funding: Department of Science and Technology, Government of Gujarat, India. Conflict of Interest: All the authors of this manuscript declare no competing interests. Ethical Approval: The present studies involving human participants were reviewed and approved by Institutional Ethical Committee of Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, and B. J. Medical College and Civil hospital, Ahmedabad, reference No. EC/Approval/38/2020.

Introduction Ayurveda takes advantage of the beneficial properties of medicinal plants. High demands in combination with inadequate availability of botanicals and a lack of knowledge with respect to their precise identification lead to adulterations in herbal products. Identification becomes more difficult in complex herbal formulations. Four different polyherbal formulations have been analyzed for the present paper. The targeted plants have different pharmacological properties for various ailments. Objective We aimed to examine the rbcL gene based plant DNA mini-barcode to identify target and non-target plants in polyherbal formulations by using high-throughput next generation sequencing. Methods Degenerate primers of the selected mini-barcode region have been identified from the literature. A blend of 30 authentic medicinal plant species was used to examine the species resolution capacity of the mini-barcode. DNA was isolated from herbal formulations, an amplicon library was prepared, and sequencing was performed on an IonS5 system. Data were analyzed using various bioinformatics tools. Results Analysis of control pooled samples revealed the optimum resolving power of the DNA mini-barcode. Data analysis of the commercial samples revealed that only one herbal formulation contained all plants and matched with listed contents. In two formulations, only 10 out of 21 and 11 out of 20 plants were detected, respectively. Additionally, several non-listed plants were also detected in these formulations. Two formulations contained >20% reads assigned to non-target plants. Overall, 21.98% of the reads were assigned to non-target plants. Conclusion The present study clearly demonstrated the successful application and potential of meta-barcoding in the quality control of complex herbal matrices. The results strongly suggest that this approach can be used in pharmacovigilance of processed herbal products.

In the current scenario, great emphasis is being made on the recovery, recycling, and reconditioning of organic solid waste. With a focus on the bioconversion of organic waste into value-added products, municipal vegetable waste was fractionated into liquid and solid part. The solid fraction was subjected to biodegradation in the presence of different microbial consortia and different enzymes were extracted. The remaining solid stuff was converted into animal feed, followed by the evaluation of its microbiological and chemical indices. Liquid fraction separated from waste was used as a crude medium to grow different bio-fertilizer strains. Among the three consortia, consortium C (Aspergillus terreus and Myrothecium verrucaria) showed the maximum production of amylase, cellulase, xylanase and pectinase after 4 days. Results of the microbiological and chemical parameters of the animal feed prepared from the fermented vegetable waste showed that the various parameters were found to be within the permissible limit. The average concentrations of heavy metals in the compost was found to be within the permissible limit of FCO standard, therefore, it can also be used for agricultural application. For using liquid extract of the vegetable waste, maximum CFU count 1.9 × 106, 1.1 × 106, and 8.7 × 10 5 was achieved in BAB 1980, BAB 662, and BAB 267 strain, respectively after 30 h of incubation. Thus, the present study demonstrated the bioconversion of vegetable waste into crude enzymes, animal feed, compost, and liquid biofertilizer.

Coconut coir (a lignin-rich, organic material) is widely used for its commercial and economic benefits. In this study, crossbred (exotic) and Kankrej (indigenous) breeds of cattle were fed diets containing 7 or 14% coconut coir. Metagenomic analyses (16S rRNA gene amplicon and shotgun sequencing) were used to characterize the microbial community in the rumen and fecal samples along with their functional capabilities. Both amplicon and shotgun analyses revealed the predominance of bacterial phyla, Bacteroidetes, Firmicutes, Actinobacteria and Fibrobacter in ruminal liquid, ruminal solid and fecal samples. 16S rRNA gene amplicon sequencing revealed a total of 18 different bacterial taxa were found to be enriched exclusively in the animals fed with 14% coir. The shotgun analysis revealed abundance of bacterial genera, Fibrobacter, Clostridium, Prevotella, Butyrivibrio, and Ruminococcus in both liquid and solid fractions of ruminal contents, while in the fecal sample, Bacteroides, Alistipes, Plaudibacter, Parabacteroides, Porphyromonas, and Victivallis and archaeal genus, Methanocorpusculum were abundant. The functional analysis based on dbCAN database suggested that among the Glycoside hydrolase family, genes that encode oligosaccharide degrading enzymes, GH3, GH13 (p-value0.05), and GH43 were abundant in the feces. In ruminal solid, cellulase encoding the GH5 family was abundant. Also, lignocellulosic binding modules encoded by the CBM family, including cellulose (CBM3) and hemicellulose binding modules (CBM32 and CBM67) were abundant. Thus, the study indicated the enrichment of lignocellulosic enzymes in ruminal contents in response to feeding the coconut coir, which could be mined for potential biofuel production and other biotechnological applications.

The incidence and severity of respiratory diseases in commercial broiler chicken flocks have increased recently in India because of intensification of the broiler industry. Viral population are predominant in respiratory tract infections and they pose continuous economic burden to poultry industry by causing severe economic losses through decreased productivity [1, 2]. To understand viral metagenome of poultry associated with respiratory infections, we performed DNA virome sequencing and data analysis of broilers from 8 districts of Gujarat State in India. We report high quality sequencing reads and highly abundant DNA viral population present in the infected broiler birds. The raw sequencing data used to perform metagenomic analysis is available in the Sequence Read Archive (SRA) under the BioProject No. PRJNA322592 and Accession No. MAUZ00000000, MAVA00000000, MAVB00000000, MAVC00000000, MAVD00000000, MAVE00000000, MAVF00000000, MAVG00000000 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA322592). Keywords: DNA Virome, Metagenomics, Next generation sequencing

The lactic acid bacterium Pediococcus acidilactici has recently been reported to help in treating constipation, diarrhea, relieving stress, and enhancing growth rate and immune response in humans, birds, fishes, and small animals. In the present study, we sequenced and analyzed the whole genome of P. acidilactici NRCC1, a novel isolate from rumen fluid of dromedary camel (Camelus dromedarius). The genome of P. acidilactici NRCC1 was assembled into 60 contigs, comprising 1,785,679 bp and 42.5% GC content. The 1705 CDS were predicted and annotated using the RAST server. The genome encodes numerous enzymes for utilization of different carbohydrates. It also harbors genes for antibiotic biosynthesis and many others which might confer probiotic properties. The comparative genome analysis with P. acidilactici DSM 20284 revealed some unique features in P. acidilactici NRCC1. Thus, the genome sequencing of P. acidilactici NRCC1 has opened up new horizons for further research in animal probiotics and feed supplements.

Most of the studies examining human milk microbiota were focused on differences in bacterial taxa in relation to birthing method, gestation time and infant gender. In this study, we aimed to understand influence of different lifestyles on milk microbiota by utilizing metagenomic approach. Milk microbiota from 15 urban women living in metropolitan city and 15 rural women living in tribal village of Gujarat, India were profiled by 16S rRNA gene sequencing. The bacterial community in human milk contained over 26 phylum, 157 family and 543 different genera. Comparison of urban and rural milk microbiota revealed that they differ in both i) highly abundant taxa, including Proteobacteria ( P = 0.008) and Firmicutes ( P = 0.046), and ii) overall microbial diversity (Shannon index, P

Breastfeeding undoubtedly provides important benefits to the mother-infant dyad and should be encouraged. Mastitis, one of the common but major cause of premature weaning among lactating women, is an inflammation of connective tissue within the mammary gland. This study reports the influence of mastitis on human milk microbiota by utilizing 16 S rRNA gene sequencing approach. We sampled and sequenced microbiome from 50 human milk samples, including 16 subacute mastitis (SAM), 16 acute mastitis (AM) and 18 healthy-controls. Compared to controls, SAM and AM microbiota were quite distinct and drastically reduced. Genera including, Aeromonas, Staphylococcus, Ralstonia, Klebsiella, Serratia, Enterococcus and Pseudomonas were significantly enriched in SAM and AM samples, while Acinetobacter, Ruminococcus, Clostridium, Faecalibacterium and Eubacterium were consistently depleted. Further analysis of our samples revealed positive aerotolerant odds ratio, indicating dramatic depletion of obligate anaerobes and enrichment of aerotolerant bacteria during the course of mastitis. In addition, predicted functional metagenomics identified several gene pathways related to bacterial proliferation and colonization (e.g. two-component system, bacterial secretion system and motility proteins) in SAM and AM samples. In conclusion, our study confirmed previous hypothesis that mastitis women have lower microbial diversity, increased abundance of opportunistic pathogens and depletion of commensal obligate anaerobes.

Mastitis is an inflammatory disease of the mammary gland, which occurs mainly because of infection. Infectious mastitis imposes significant economic losses throughout the world. Metagenomic approach was used to investigate bacterial diversity using 16S rRNA gene amplicon sequencing of clinical and subclinical mastitis affected buffalo milk. The data were analyzed using best hit approach through MG-RAST having 95% of the total reads assigned to bacteria. However, about 4% of all analyzed sequences were found to be not assigned to any known bacterial group which suggests that the disease may involve a community of not yet described bacterial groups. Sequences predominantly aligned with the phyla 57% Firmicutes followed by 16% Proteobacteria . At the family level, Staphylococcaceae and Enterococcaceae were predominated in samples from subclinical mastitis, whereas Streptococcaceae was predominated in samples from clinical mastitis. Reads were also assigned to uncultured bacterium indicating that they may also be associated with the etiology of mastitis. Thus the use of metagenomic pyrosequencing of the 16S rRNA may be considered to be an important tool to advance our knowledge regarding the pathogenesis of mastitis in buffalo.

Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.

Objective Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and “white chicks” condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens. Methods Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein. Results The consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5′-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3′-UTR which harboured two corona virus stem loop II like “s2m” motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74–98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes. Electronic supplementary material The online version of this article (doi:10.1007/s11259-016-9673-6) contains supplementary material, which is available to authorized users.

Members of the genus Aspergillus are extensively studied ascomycetes because of their ability to synthesize high value-added compounds and enzymes of industrial interest. Precise whole genome assembly and gene annotation are significant for gene functional analyses. Here, we report the draft genome sequencing, assembly and whole genome analysis of Aspergillus terreus P14_T3, isolated from rumen sample of cattle fed with coconut-coir. A total of 13,340 protein-coding genes were predicted, among them 493 are involved in degradation of complex carbohydrate polysaccharides. Further, it was found that 29 genes, encoding β-glucosidase belong to Glycosyl hydrolase (GH) family 1 (3 gene), 3 (17 gene), 5 (4 gene), 17 (3 gene), 132 (2 gene). The tertiary structure of all the β-glucosidases was designed by homology modeling; modeled structure AtBgl1.3 (GH1), AtBgl3.1 (GH3), AtBgl5.4 (GH5), AtBgl17.1 (GH17) show classical (α/β) TIM-like barrel motif. Molecular docking of different β-glucosidases with cellobiose revealed that conserved amino acids i.e. Glu, Trp, Arg, His, Tyr and Asp are taking part in substrate hydrolysis. Moreover, some other amino acids i.e. Ser, Phe, Gln and Asn are found to be involved in hydrogen bond formation and catalysis. These findings may provide valuable insights in designing β-glucosidases with higher cellulose-hydrolyzing efficiency.

Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P < 0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P < 0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis. (C) 2018 Elsevier GmbH. All rights reserved.

Background The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence. Methods Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing. Results Each caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p

Microbial colonisation in the forestomach of a ruminant is one of the most crucial factors in determining many of its physiological developments and digestive capabilities. The present study attempts to identify establishment pattern of microbes in relation to food, age and rumen development in the buffalo calves at every fortnight interval from birth to 6 months of age, followed by every month till animals became 1 year of age. Diversity study based on 16S rRNA gene sequencing identified rapidly changing bacterial population during initial 60 days of life, which got assemblage as rumen became physiologically mature with increasing age of animals. A lactate fermenting aerobic to facultative anaerobic genera found during initial 30 days of life were expeditiously replaced by strict anaerobic cellulolytic bacterial population with increasing age. The study confirms that initial colonisation mainly depends on the oral cavity and skin of the mother, followed by the surrounding environment and feed offered, which is reversed in order once animal gets older. Some of the well-described genera based on culture-dependent studies like Ruminococcus spp. were found to be in lesser proportion suggesting an additional role of other microbes or niche in cellulose degradation. We report the presence of Porphyromonas spp. and Mannheimia glucosidal for the first time in bovine infants.

Cellulase hydrolyses the cellulose by cleaving the β-1,4-linkages to produce mono-, oligo- and shorter polysaccharide units. These enzymes have applications in various industries such as pulp and paper, laundry, food and feed, textile, brewing industry and in biofuel production. In the present study we have cloned acid-cellulase gene (Cel-1) from the fosmid library of buffalo rumen metagenomic DNA and functionally expressed it in Escherichia coli. The ORF encoding cellulase consisted of 1176-bp, corresponding to protein of 391 amino acid and has catalytic domain belonging to glycosyl hydrolase family 5. The purified protein has a molecular weight of 43-kDa on SDS-PAGE and its expression was confirmed by western blotting. The tertiary structure of the cellulase (Cel-1) showed a classical (α/β) TIM-like barrel motif. Model surface charge of Cel-1 predicted that surface near active site was mostly negative which might be responsible for the stability of enzyme at lower pH. The pH and temperature for maximum enzyme activity were 4.5 and 45°C respectively. Various metal ions enhanced the enzyme activity and in presence of Mn+2 activity was significantly increased. Cel-1 hydrolyzed pre-treated wheat straw and released reducing sugars (62.60%). These desirable properties of Cel-1 make it attractive for the bioconversion of biomass.

Tuberculosis (TB), caused by Mycobacterium tuberculosis is an infectious deadly disease and the treatment of which is one of the most severe challenges at the global level. Currently more than 20 chemical medications are described for the treatment of TB. Regardless of availability of several drugs to treat TB, the causative agent, M. tuberculosis is nowadays getting resistant toward the conventional drugs and leading to conditions known as Multidrug-resistant tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB). This situation has terrified the global health community and raised a demand for new anti-tuberculosis drugs. Medicinal plants have been used to cure different common as well as lethal diseases by ancient civilizations due to its virtue of variety of chemical compounds which may have some important remedial properties. The aim of the present review is to focus the anti-tubercular medicinal plants native to India as well as the plants effective against MDR or XDR-TB across the globe. In the present review, we have addressed 25 medicinal plants for TB and 16 plants effective against MDR-TB testified from India and 23 herbal plants described for MDR-TB across the world during 2011-2015. These herbal plants can serve as promising candidates for developing novel medications to combat multidrug resistant M. tuberculosis.

Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G. herbaceum on pyrosequencing and its analysis. About 1.38 million raw and 1.12 million quality trimmed reads were obtained followed by de novo assembly-generated 20,125 unigenes containing 14,882 coding sequences (CDs). BLASTx-based test of homology indicated that A1-derived transcripts shared a high similarity with Gossypium arboreum (A2). Functional annotation of the CDs using the UniProt categorized them into biological processes, cellular components, and molecular function, COG classification showed that a large number of CDs have significant homology in COG database (6215 CDs), and mapping of CDs with Kyoto Encyclopedia of Genes and Genomes (KEGG) database generated 200 pathways ultimately showing predominant engagement in the fiber development process. Transcription factors were predicted by comparison with Plant Transcription Factor Database, and their differential expression between stages exposed their important regulatory role in fiber development. Differential expression analysis based on reads per kilobase of transcript per million mapped reads (RPKM) value revealed activities of specific gene related to carbohydrate and lipid synthesis, carbon metabolism, energy metabolism, signal transduction, etc., at four stages of fiber development, and was validated by qPCR. Overall, this study will help as a valuable foundation for diploid cotton fiber improvement.

Nematode-trapping fungi are well known for their inherent potential to trap and kill nematodes using specialized trapping devices. However, the molecular mechanisms underlying the trapping and subsequent processes are still unclear. Therefore, in this study, we examined differential genes expression in two nematode-trapping fungi after baiting with nematode extracts. In Arthrobotrys conoides, 809 transcripts associated with diverse functions such as signal transduction, morphogenesis, stress response and peroxisomal proteins, proteases, chitinases and genes involved in the host-pathogen interaction showed differential expression with fold change (>±1.5 fold) in the presence of nematode extract with FDR (p-value

The advent of metagenomics using Next-Generation Sequencing (NGS) has led to the acquisition of unprecedented quantities of bacterial sequence data. One use for these data is the recovery of complete genomes of uncultivable, and thus uncharacterised, organisms. The separation of genome from metagenomics data remains challenging, however genomes of several novel lineages and organisms have been reconstructed successfully. Here, we report the use of NGS to reconstruct the draft genome of a previously undescribed bacterium from the caecal microbiome of domestic chickens. This bacterium has a genome size of 2.38 Mb, a 52.13% GC content and 16S rRNA gene phylogenetic analysis indicates that it belongs to a recently recognised family of anaerobes, the Muribaculaceae belonging to Bacteroidetes phylum. Bacteroidetes is one of the major phyla in chicken caecum amounting to 12%–61%. The caecum is a major site of intestinal fermentation that harbours a diverse collection of anaerobic bacteria. From direct genome annotation, this newly identified bacterium is predicted to utilise starch as its primary carbon source, as evidenced by the large number of amylases encoded within its genome: we thus propose the name Candidatus Amulumruptor caecigallinarius. The importance of caecal carbohydrate metabolism and fermentation to the overall health, welfare and productivity of the chicken predicts an important role for this novel Candidatus bacterium in food security.

Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes , exhibits azoreduction of textile dyes. Here, we report the draft genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with xenobiotic compound degradation.

Two nematode trapping fungi were isolated from the arable soil samples collected from district Anand (Gujarat) India and identified on the basis of their culture-morphological characteristics and 18S rRNA gene sequencing as Arthrobotrys conoides (GenBank accession No. JX979095) and Duddingtonia flagrans (GenBank accession No. JX979094). These fungal isolates were assessed for their trapping efficiency against root knot disease causing nematode Meloidogyne spp., isolated from the infected tomato plants. When incubated with nematodes for 24 hr, the trapping efficiency of A. conoides and D. flagrans was 92–95 and 22–29%, respectively. Growth conditions with respect to medium, temperature and pH were also optimized. This study showed that A. conoides is a promising candidate to control root-knot nematodes. Phylogenetic relationship with other nematophagous fungi showed that isolates formed monophyletic clade with other nematode trapping fungi as well.