• Volume 44, Issue 5

      October 2019

    • Editorial


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    • Microbiota of spent nuclear fuel pool water with emphasis on their biofilm forming ability on stainless steel (SS-304L)


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      Spent nuclear fuel (SNF) pool is an essential unit of a nuclear power plant infrastructure, where radioactive fuel rods arekept for cooling and shielding, before reprocessing. This study explored the presence of bacteria in SNF pool water withemphasis on their capability to form biofilms on pool wall cladding material stainless steel (SS-304L). Bacteria wereisolated from SNF pool water and were characterized using 16S rRNA gene sequencing. The six bacterial isolates (Bacillussubtilis, Staphylococcus sps., S. arlettae, S. epidermidis, S. auricularis and Chryseobacterium gleum) can grow and formbiofilms at very low nutrient condition as well as in chronic radioactivity. The bacterial isolates formed biofilm on SS-304Land glass. However, the biofilm parameters assessed by CLSM microscopy showed that the strains preferred SS-304Lsurface for biofilm formation. On SS-304L, the maximum biomass (0.45 lm3/lm2) was formed by S. arlettae whencompared to maximum biomass (0.054 lm3/lm2) by Staphylococcus sp., on glass. Maximum biofilm thickness on SS-304L was observed by Staphylococcus sp. (8.81 lm) when compared to that of S. epidermidis (4.16 lm) on the glasssurface. The biofilm formation on SS-304L surface suggests the possible risk of microbial-induced corrosion of SNF poolcladding material. This study highlights the need for mandatory monitoring of microbial biofilm formation in an extremeenvironment such as SNF pool.

    • Linking microbial diversity with ecosystem functioning through a trait framework


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      Trait-based microbial biogeography provides a path for the mechanistic understanding of relationships between microbialdiversity and ecosystem functioning. In this mini-review, we identify the scenarios in which to use traits to characterize themicrobial community and propose a simple trait-based conceptual framework to link microbial communities withecosystem functions.

    • Connect between gut microbiome and diseases of the human eye


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      Implicating dysbiosis of gut microbiome in digestive tract diseases/diet-related diseases (obesity, inflammatory boweldisease, enterocolitis, diabetes, etc.) may be expected. However, when gut microbiome dysbiosis is implicated in extraintestinaldiseases like cancers, muscular dystrophy, mental disorders, vaginosis, etc., it is all the more challenging. Anadditional challenge would be to ascertain the role of gut microbiome in ocular diseases, which are as remote as the brain.The present review highlights studies that establish the connect between gut microbiome dysbiosis and inflammatory oculardiseases such as uveitis, bacterial keratitis, fungal keratitis, etc.

    • Successful strategies for human microbiome data generation, storage and analyses


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      Current interest in the potential for clinical use of new tools for improving human health are now focused on techniques forthe study of the human microbiome and its interaction with environmental and clinical covariates. This review outlines theuse of statistical strategies that have been developed in past studies and can inform successful design and analyses ofcontrolled perturbation experiments performed in the human microbiome. We carefully outline what the data are, theirimperfections and how we need to transform, decontaminate and denoise them. We show how to identify the importantunknown parameters and how to can leverage variability we see to produce efficient models for prediction and uncertaintyquantification. We encourage a reproducible strategy that builds on best practice principles that can be adapted for effectiveexperimental design and reproducible workflows. Nonparametric, data-driven denoising strategies already provide the beststrain identification and decontamination methods. Data driven models can be combined with uncertainty quantification toprovide reproducible aids to decision making in the clinical context, as long as careful, separate, registered confirmatorytesting are undertaken. Here we provide guidelines for effective longitudinal studies and their analyses. Lessons learnedalong the way are that visualizations at every step can pinpoint problems and outliers, normalization and filtering improvepower in downstream testing. We recommend collecting and binding the metadata and covariates to sample descriptors andrecording complete computer scripts into an R markdown supplement that can reduce opportunities for human error andenable collaborators and readers to replicate all the steps of the study. Finally, we note that optimizing the bioinformatic andstatistical workflow involves adopting a wait-and-see approach that is particularly effective in cases where the features suchas ‘mass spectrometry peaks’ and metagenomic tables can only be partially annotated.

    • Understanding the association between the human gut, oral and skin microbiome and the Ayurvedic concept of prakriti


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      Ayurveda is one of the ancient systems of medicine which is widely practised as a personalized scientific approach towardsthe general wellness. Ayurvedic prakriti is broadly defined as the phenotypes which are determined on the basis of physical,psychological and physiological traits irrespective of their social, ethnic, dietary and geographical stature. Prakriti is theconstitution of a person, which comprises vata, pitta, and kapha and is a key determinant of how one individual is differentfrom the other. Human microbiome is considered the ‘latest discovered’ human organ and microbiome research reiteratesthe fundamental principles of Ayurveda for creating a healthy gut environment by maintaining the individual-specificmicrobiome. Hence, it is important to understand the association of human microbiome with the Ayurvedic prakriti of anindividual. Here, we provide a comprehensive analysis of human microbiome from the gut, oral and skin samples of healthyindividuals (n=18) by 16S rRNA gene-based metagenomics using standard QIIME pipeline. In the three different prakritisamples differential abundance of Bacteroides, Desulfovibrio, Parabacteroides, Slackia, and Succinivibrio was observed inthe gut microbiome. Analysis also revealed prakriti-specific presence of Mogibacterium, Propionibacterium, Pyramidobacter,Rhodococcus in the kapha prakriti individuals Planomicrobium, Hyphomicrobium, Novosphingobium in the pittaprakriti individuals and Carnobacterium, Robiginitalea, Cetobacterium, Psychrobacter in the vata prakriti individuals.Similarly, the oral and skin microbiome also revealed presence of prakriti-specific differential abundance of diversebacterial genera. Prakriti-specific presence of bacterial taxa was recorded and only 42% microbiome in the oral samples and52% microbiome in the skin samples were shared. Bacteria known for preventing gut inflammation by digesting theresistant starch were abundant in the pitta prakriti individuals, who are more prone to develop gut-inflammation-relateddisorders. In summary, human gut, oral and skin microbiome showed presence or high abundance of few bacterial taxaacross three prakriti types, suggesting their specific physiological importance.

    • Insights into the gastrointestinal tract microbiomes of Indian population


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      Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in theGIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- andmicronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developmentsand resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem variesgreatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked withdietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understandinga holistic picture of GIT microbiome of healthy people living across geography and identifying population specific

      ‘keystone’ taxa is of immense importance for identifying microbial species that may provide protection against chronic andmetabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand thevaried efficacy of different drugs and vaccines in different populations. India is the home of more than 1.36 billion peoplebelonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbialsignatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.

    • Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion


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      Microbial community structure of crude petroleum oil (CP)- and refined petroleum oil (RP)-contaminated soil wasinvestigated. The taxonomical and functional diversity of such soils can be a great source of information about microbialcommunity and genes involved in petroleum hydrocarbon (PHC) degradation. In this study, microbial diversity of soilscontaminated by RP from urban biome of Pune, India, and CP from agricultural biome of Gujarat, India, were assessed by16S rRNA amplicon sequencing on Illumina MiSeq platform. Association between the soil microbial community and thephysicochemical parameters were investigated for their potential role. In RP- and CP-contaminated soils, the microbiomeanalysis showed Proteobacteria as most dominant phylum followed by Actinobacteria. Interestingly, Firmicutes were mostprevailing in a CP-contaminated sample while they were least prevailing in RP-contaminated soils. Soil moisture content,total organic carbon and organic nitrogen content influenced the taxa diversity in these soils. Species richness was more inRP as compared to CP soils. Further prediction of metagenome using PICRUSt revealed that the RP and CP soils containmicrobial communities with excellent metabolic potential for PHC degradation. Microbial community contributing to genesessential for soil health improvement and plant growth promotion was also gauged. Our analysis showed promising resultsfor future bioaugmentation assisted phytoremediation (BAP) strategies for treating such soils.

    • Microbiome data science


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      Best practices from open data science are spreading across research fields, providing new opportunities for research andeducation. Open data science emphasizes the view that digitalization is enabling new forms of resource sharing, collaborationand outreach. This has the potential to improve the overall transparency and efficiency of research. Microbiomebioinformatics is a rapidly developing area that can greatly benefit from this progress. The concept of microbiome datascience refers to the application of best practices from open data science to microbiome bioinformatics. The increasingavailability of open data and new opportunities to collaborate online are greatly facilitating the development of this field. Amicrobiome data science ecosystem combines experimental research data with open data processing and analysis andreproducible tutorials that can also serve as an educational resource. Here, we provide an overview of the current status ofmicrobiome data science from a community developer perspective and propose directions for future development of thefield.

    • Vaginal microbiota in pregnancy: Role in induction of labor and seeding the neonate’s microbiota?


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      Compared to other human microbiota, vaginal microbiota is fairly simple with low bacterial diversity and high relativeabundance of Lactobacillus species. Lactobacillus dominance is even more pronounced during pregnancy. Genetic factors,such as ethnicity, along with environmental, individual and lifestyle factors all have an impact on vaginal microbiotacomposition. The composition of the vaginal microbiota appears to play an important role in pregnancy as recent studieshave linked it to adverse obstetric outcomes such as preterm birth, a leading cause of neonatal morbidity and mortalityworldwide. However, the same vaginal microbiota does not seem to cause the same response in all women, calling forfuture research to fully understand the complex host–microbiota interplay in normal and complicated pregnancies.

    • Homeostasis and dysbiosis of the gut microbiome in health and disease


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      The human gastrointestinal tract (GIT) harbors taxonomically and functionally complex microbial ecosystem. The compositionof the microbial species in the GIT ecosystem varies among individuals and throughout development. Bothenvironmental factors as well as host genetics influence the composition and homeostasis of GIT microbiome. Intrinsic GITmicrobiome can be characterized in terms of diversity, richness, dynamics and resilience. In healthy individual, microbialcommunities maintain homeostatic equilibrium and are resistant against perturbations. The resilience and resistance toperturbations of the GIT microbial ecosystem are robust but not absolute. Several factors can affect the homeostaticequilibrium of GIT microbiome and lead to dysbiotic microbiome configuration. Taxonomic and/or functional dysbiosis inthe GIT microbiome is associated with numerous health disorders like inflammatory bowel disease (IBD), malnutrition,metabolic disorders, asthma and neurodegenerative diseases. In this review, we discuss our current understanding ofhomeostasis and dysbiosis of the microbial ecology in the human gut and health disorders that are associated with themicrobiome dysbiosis.

    • Decoding the microbiome for the development of translational applications: Overview, challenges and pitfalls


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      Recent studies have highlighted the potential of ‘translational’ microbiome research in addressing real-world challengespertaining to human health, nutrition and disease. Additionally, outcomes of microbiome research have also positivelyimpacted various aspects pertaining to agricultural productivity, fuel or energy requirements, and stability/preservation ofvarious ecological habitats. Microbiome data is multi-dimensional with various types of data comprising nucleic andprotein sequences, metabolites as well as various metadata related to host and or environment. This poses a major challengefor computational analysis and interpretation of data to reach meaningful, reproducible (and replicable) biological conclusions.In this review, we first describe various aspects of microbiomes that make them an attractive tool/target fordeveloping various translational applications. The challenge of deciphering signatures from an information-rich resourcelike the microbiome is also discussed. Subsequently, we present three case-studies that exemplify the potential of microbiome-based solutions in solving real-world problems. The final part of the review attempts to familiarize readers with theimportance of a robust study design and the diligence required during every stage of analysis for achieving solutions withpotential translational value.

    • Visual exploration of microbiome data


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      A dramatic increase in large-scale cross-sectional and temporal-level metagenomic experiments has led to an improvedunderstanding of the microbiome and its role in human well-being. Consequently, a plethora of analytical methods has beendeveloped to decipher microbial biomarkers for various diseases, cluster different ecosystems based on microbial content,and infer functional potential of the microbiome as well as analyze its temporal behavior. Development of user-friendlyvisualization methods and frameworks is necessary to analyze this data and infer taxonomic and functional patternscorresponding to a phenotype. Thus, new methods as well as application of pre-existing ones has gained importance inrecent times pertaining to the huge volume of the generated microbiome data. In this review, we present a brief overview ofsome useful visualization techniques that have significantly enriched microbiome data analytics.

    • Repeated mild traumatic brain injury affects microbial diversity in rat jejunum


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      Traumatic brain injuries (TBI) manifest into post-traumatic stress disorders such as anxiety comorbid with gut ailments. Theperturbations in gut microbial communities are often linked to intestinal and neuropsychological disorders. We havepreviously reported anxiety and abnormalities in gut function in mild TBI (MTBI)-exposed rats. The current studydemonstrates the changes in gut microbiome of MTBI-exposed animals and discusses its implications in intestinal healthand behaviours. The rats were subjected to repeated MTBI (rMTBI) and microbial composition in jejunum was examinedafter 6 h, 48 h and 30 days of rMTBI. Significant reduction in bacterial diversity was observed in the rMTBI-exposedanimals at all the time points. Principal coordinate analysis based on weighted UniFrac distances indicated substantialdifferences in gut microbial diversity and abundances in rMTBI-exposed animals as compared to that in healthy controls.The abundance of Proteobacteria increased dramatically with reciprocal decrease in Firmicutes after rMTBI. At the genuslevel, Helicobacter, Lactobacillus, Campylobacter, and Streptococcus were found to be differentially abundant in thejejunum of rMTBI-exposed rats as compared to sham controls indicating profound dysbiosis from the healthy state.Furthermore, substantial depletion in butyrate-producing bacterial communities was observed in rMTBI-exposed animals.These results suggest that the traumatic stress alters the gut microbiome with possible implications in gut health andneuropsychopathology.

    • Antimicrobial resistance pattern of microorganisms isolated and identified from Godavari River across the mass gathering event


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      The Kumbh Mela is considered the world’s largest mass gathering event (MGE). It represents a unique anthropogenicburden on the river ecosystem and may confer antimicrobial resistance among microbial communities. The present studyexplains the characterization of microbial isolates associated with Godavari River under the advent of the mass bathingevent using culture dependent approach. The isolates were identified by sequencing of 16S rRNA gene and ITS region.Further, the isolates were screened for antibiotic susceptibility against 22 antibiotics using disc diffusion method. A total of63 bacterial and 21 fungal isolates were isolated under the temporal variation of the event. Kocuria and Staphylococcuswere the most prevalent bacterial genera in the samples collected before and during the event, while Meyerozyma andCandida predominate among fungal communities. A group of antibiotics impeding the bacterial protein synthesis werefound to be most effective against C67% of bacterial isolates. However, C37–67% of isolates could escape the action ofinhibitors of bacterial cell wall synthesis. Moreover, bacterial isolates belonging to genera Acinetobacter, Corynebacteriumand Brevibacterium showed higher resistance towards the antibiotics. Observations from the current study suggest likelymicrobial taxa as targets to mitigate the waterborne infections during the MGE.

    • A new uranium bioremediation approach using radio-tolerant Deinococcus radiodurans biofilm


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      Deinococcus radiodurans is the most radiation-tolerant organism ever known. It has gained importance in recent years as apotential candidate for bioremediation of heavy metals, especially the radioactive type. This study investigates the efficiencyof a recombinant D. radiodurans (DR1-bf?) strain with an ability to form biofilm for uranium remediation. Themodified Arsenazo III dye method was used to estimate the uranium concentration. Uranyl nitrate aqueous solution wasgenerated during the operation of nuclear fuel reprocessing. The D. radiodurans biofilm (DR1-bf?) grown in the presenceof 20 mM Ca2? showed remarkable ability of uranyl ion removal. DR1-bf? (?Ca2?) biofilm removed *75±2% of1000 mg/L uranium within 30 min post-treatment from uranyl nitrate aqueous solution. Uranium removal rate was alsofound to be directly proportional to biofilm age. This study discusses the ability of D. radiodurans biofilm in uraniumremoval.

    • A robust method for nucleic acid extraction from fabrics to study bacterial diversity


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      The importance of studying microbial load on fabrics has been recently realized with reports on fabrics being a source ofspread of infection in medical and hospitality sectors. However, methodological limitations have restricted the analysis ofmicrobial diversity on fabrics. Hence, the study aimed to develop a robust method for extraction of DNA from differenttypes of fabrics. Bacterial community profiles could be successfully generated with DNA extracted from real life samples,together with identification of different bacterial genera on fabrics. The study opens up venues to study effect of environmentalfactors on microbial load on fabrics. Also, such a technique will aid correlation between microbial load and typesof fabric so as to come up with recommendation for fabrics bearing minimal microbial load for medical and hospitalitysectors.

    • Cellulolytic, amylolytic and xylanolytic potential of thermophilic isolates of Surajkund hot spring


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      A total of 41 isolates were obtained from various samples (soil, mud, and water) of Surajkund hot spring, Jharkhand, atthree different isolation temperatures of 50 deg C, 60 deg C, and 70 deg C. However, our interest was in the thermophilic strains thatwere isolated at 60 deg C and 70 deg C. Four isolates at 70 deg C (BITSNS038, BITSNS039, BITSNS040, BITSNS041) are theproducers of thermozymes, namely amylase, xylanase, and cellulase, respectively. The highlights of the present study alsoshowed that three out of four isolates demonstrated all three enzymatic activities, i.e. amylolytic, xylanolytic and cellulolyticon agar plate assay conditions at 70 deg C. One of the isolates, BITSNS038, was further chosen for phenotypiccharacterization as well as 16S rRNA gene sequencing and was affiliated to Geobacillus icigianus. The presence ofGeobacillus icigianus was reported first time from hot spring, Surajkund, which showed amylolytic index of 1.58,xylanolytic index of 1.5 and cellulolytic index of 2.3 based on plate assay, and amylase activity of 0.81 U/mL, xylanaseactivity of 0.72 U/mL and very less cellulase activity of 0.15 U/mL after 24 h of growth in submerged conditions. Oneisolate at 60 deg C BITSNS024 was found to exhibit maximum amylase activity with an enzymatic index value of 3.5 and wasidentified as Anoxybacillus gonensis.

    • Multi-resistant biofilm-forming pathogens on the International Space Station


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      The International Space Station (ISS) is a confined and closed habitat with unique conditions such as cosmic radiation, andmicrogravity. These conditions have a strong effect on the human and spacecraft microflora. They can affect the immuneresponse of the crew-members, thus posing a threat to their health. Microbial diversity and abundance of microorganismsfrom surfaces, air filters and air samples on the ISS have been studied. Enterobacteriaceae, Bacillus spp., Propionibacteriumspp., Corynebacterium spp., and Staphylococcus spp. were among the most frequently isolated bacteria. Microbialgrowth, biofilm formation, stress response, and pathogenicity are affected by microgravity. Increased resistance toantibiotics in bacteria isolated from the ISS has often been reported. Enterococcus faecalis and Staphylococcus spp. isolatesfrom the ISS have been shown to harbor plasmid-encoded transfer genes. These genes facilitate the dissemination ofantibiotic resistances. These features of ISS-pathogens call for novel approaches including highly effective antimicrobialswhich can be easily used on the ISS. A promising material is the antimicrobial surface coating AGXX(R), a self-recyclingmaterial consisting of two noble metals. It drastically reduced microbial growth of multi-resistant human pathogens, such asstaphylococci and enterococci. Further novel approaches include the application of cold atmospheric plasma for thesterilization of spacecrafts.

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