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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.

Aim: To study the efficacy and adverse events after use of Anti Snake Venom (ASV) and note its usagepatternMethods: This prospective observational study included 97 cases of snake bite admitted to Indira GandhiGovernment General Hospital and Postgraduate Institute, Poducherry from June 2016 to December 2017.Adverse reactions to ASV and clinical response parameters like number of vials of ASV needed, time toresponse, hospital stay were analysedResults: Of the 97 cases enrolled and 96 analysable, 59 cases had hemotoxic , 12 neurotoxic, 9 a combinationof both and 16 had local envenomation, The mean number of vials used( 25.92 +/-12.97), time to controlenvenomation( 35.48+/- 22.03 hours) and duration of hospital stay ( 5.79 +/-4.89 days) was not significantlydifferent for any particular type of envenomation16 patients suffered 49 adverse events, 34 being mild, 10 moderate and 5 severe. The symptom cluster ofitching, urticaria, was the most common, seen in 9 patients. This was accompanied by a permutation oftachycardia with colic, vomiting, nausea and diarrhoea. Most were managed by giving an additional dose ofhydrocortisone or antihistamine or both. None had to be administered adrenaline.Conclusions: The ASV brand used, was well tolerated, and the number of adverse events were less thanthose reported in earlier studies. Authors conclude that the National Guidelines are applicable in majority ofthe cases but due consideration must be given to the clinician’s judgement in individual cases

Additional file 1. Exercise Therapy Burden Questionnaire.

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.

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.

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.

Purpose: To determine the prevalence and risk factors of dry eye disease in Geriatric (>65 years) and Pre-geriatric (40-65 years) populations and to compare the same between both the groups. Setting: Indira Gandhi Government General Hospital and Post graduate Institute, Puducherry, India Design: Prospective, cross-sectional, clinical study Methods: All patients above 40 years attending the out-patient departments were given the Mc Monnie and Ho screening questionnaire for dry eye symptoms and risk factors. Those with a score of > 14.5 were further evaluated using Ocular Surface Disease Index (OSDI) severity subjective questionnaire, and objective clinical tests inclusive of Schirmer’s test, Meibomian Gland Dysfunction (MGD) assessment, Tear Film Break Up Time (TBUT), Fluorescein staining and Impression cytology. The prevalence, risk factors, clinical signs and symptom-sign correlation were determined and compared between the two groups. Results: Among the 1029 patients screened, the prevalence of dry eye was 9.9%, being significantly higher among the geriatric (15.4%) versus pre-geriatric group (7.7%), p

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.