Metagenomics

Illustrated Dictionary of Parasitology in the Post-Genomic Era Author: Hany M. Elsheikha and Edward L. Jarroll (Published: 2017) "a guide for students, academic staff, medical and veterinarian professionals" (ProtoView); "an extensive and comprehensive glossary of contemporary concepts, terminologies, and vocabulary in modern parasitology" (Doodys); "a pure pleasure to explore and discover" (Epidemiol. Infect.); "highly recommended" (Biotechnol. Agron. Soc. Environ.

Metagenomic techniques are used to analyse bacterial communities allowing both culturable and unculturable species to be represented. However, the screening of oral metagenomic samples can be hindered by high animal host DNA content. This study evaluated methods for the reduction of human DNA concentrations within oral metagenomic samples.

Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species' growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.

Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB-and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols. The SDS-based protocol enabled access to the highest sorghum endophytic diversities. Therefore, "SDS-extracted" sorghum root and stem microbiome diversities were analysed via 454 pyrosequencing, and this revealed that the two tissues harbour significantly different endophytic communities. Nevertheless, both communities are dominated by agriculturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas and Stenotrophomonas; which have previously been shown to play a role in plant growth promotion. This study shows that DNA extraction protocols introduce biases in culture-independent studies of environmental microbial communities by influencing the mDNA quality, which impacts the microbial diversity analyses and evaluation. Using the broad-spectrum SDSbased DNA extraction protocol allows the recovery of the most diverse endophytic communities associated with sorghum tissues and, as such, establishes a reliable basis for future study of endophytic communities.

Amplification of minute quantities of DNA is a fundamental challenge in low-biomass metagenomic and microbiome studies because of potential biases in coverage, guanine-cytosine (GC) content, and altered species abundances. Whole genome amplification (WGA), although widely used, is notorious for introducing artifact sequences, either by amplifying laboratory contaminants or by nonrandom amplification of a sample's DNA. In this study, we investigate the effect of REPLI-g multiple displacement amplification (MDA; Qiagen, Valencia, CA, USA) on sequencing data quality and species abundance detection in 8 paired metagenomic samples and 1 titrated, mixed control sample. We extracted and sequenced genomic DNA (gDNA) from 8 environmental samples and compared the quality of the sequencing data for the MDA and their corresponding non-MDA samples. The degree of REPLI-g MDA bias was evaluated by sequence metrics, species composition, and crossvalidating observed species abundance and species diversity estimates using the One Codex and MetaPhlAn taxonomic classification tools. Here, we provide evidence of the overall efficacy of REPLI-g MDA on retaining sequencing data quality and species abundance measurements while providing increased yields of high-fidelity DNA. We find that species abundance estimates are largely consistent across samples, even with REPLI-g amplification, as demonstrated by the Spearman's rank order coefficient (R 2. 0.8). However, REPLI-g MDA often produced fewer classified reads at the species, genera, and family level, resulting in decreased species diversity. We also observed some areas with the PCR "jackpot effect," with varying input DNA values for the Metagenomics Research Group (MGRG) controls at specific genomic loci. We visualize this effect in whole genome coverage plots and with sequence composition analyses and note these caveats of the MDA method. Despite overall concordance of species abundance between the amplified and unamplified samples, these results demonstrate that amplification of DNA using the REPLI-g method has some limitations. These concerns could be addressed by future improvements in the enzymes or methods for REPLI-g to be considered a .99% robust method for increasing the amount of high-fidelity DNA from low-biomass samples or at the very least, accounted for during computational analysis of MDA samples.

In recent years, the application of approaches for harvesting DNA from the environment, the so-called, 'metagenomic approaches' has proven to be highly successful for the identification, isolation and generation of novel enzymes. Functional screening for the desired catalytic activity is one of the key steps in mining metagenomic libraries, as it does not rely on sequence homology. In this mini-review, we survey high-throughput screening tools, originally developed for directed evolution experiments, which can be readily adapted for the screening of large libraries. In particular, we focus on the use of in vitro compartmentalization (IVC) approaches to address potential advantages and problems the merger of cultureindependent and IVC techniques might bring on the mining of enzyme activities in microbial communities.

Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from > 1,500 public metagenomes. All genomes are estimated to be ≥ 50% complete and nearly half are ≥ 90% complete with ≤ 5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by > 30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.

Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagen...

Recent advances in nucleic acid sequencing technologies, referred to as 'next-generation' sequencing (NGS), have produced a true revolution and opened new perspectives for research and diagnostic applications, owing to the high speed and throughput of data generation. So far, NGS has been applied to metagenomics-based strategies for the discovery of novel viruses and the characterization of viral communities. Additional applications include whole viral genome sequencing, detection of viral genome variability, and the study of viral dynamics. These applications are particularly suitable for viruses such as human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, whose error-prone replication machinery, combined with the high replication rate, results, in each infected individual, in the formation of many genetically related viral variants referred to as quasi-species. The viral quasi-species, in turn, represents the substrate for the selective pressure exerted by the immune system or by antiviral drugs. With traditional approaches, it is difficult to detect and quantify minority genomes present in viral quasi-species that, in fact, may have biological and clinical relevance. NGS provides, for each patient, a dataset of clonal sequences that is some order of magnitude higher than those obtained with conventional approaches. Hence, NGS is an extremely powerful tool with which to investigate previously inaccessible aspects of viral dynamics, such as the contribution of different viral reservoirs to replicating virus in the course of the natural history of the infection, co-receptor usage in minority viral populations harboured by different cell lineages, the dynamics of development of drug resistance, and the re-emergence of hidden genomes after treatment interruptions. The diagnostic application of NGS is just around the corner.

The open-source de novo protein-level assembler, Plass (https://plass.mmseqs.com), assembles six-frame-translated sequencing reads into protein sequences. It recovers 2-10 times more protein sequences from complex metagenomes and can assemble huge datasets. We assembled two redundancy filtered reference protein catalogs, 2 billion sequences from 640 soil samples (soil reference protein catalog) and 292 million sequences from 775 marine eukaryotic metatran-scriptomes (marine eukaryotic reference catalog), the largest free collections of protein sequences.

Biodiesel, as an alternative fuel, is gradually receiving more popularity for use in internal combustion engines. However questions continue to arise with regard to its compatibility with elastomeric materials. The present work aims to investigate the comparative degradation of physical properties for different elastomers [e.g. ethylene propylene diene monomer (EPDM), silicone rubber (SR), polychloroprene (CR), polytetrafluroethylene (PTFE) and nitrile rubber (NBR)] upon exposure to diesel and palm biodiesel. Static immersion tests in B0(diesel), B10 (10% biodiesel in diesel), B20, B50 and B100(biodiesel) were carried out at room temperature (25 °C) for 1000 h. Different physical properties like, changes in weight and volume, hardness and tensile strength were measured at every 250 h of immersion time. Compositional changes in biodiesel due to exposure of different elastomers were investigated by Gas chromatography mass spectroscopy (GCMS). The overall sequence of compatible elastomers in palm biodiesel is found to be PTFE > SR > NBR > EPDM > CR.

http://www.sciencedirect.com/science/article/pii/S0360544210007139

Polyurethanes (PU) are the sixth most produced plastics with around 18-million tons in 2016, but since they are not recyclable, they are burned or landfilled, generating damage to human health and ecosystems. To elucidate the mechanisms that landfill microbial communities perform to attack recalcitrant PU plastics, we studied the degradative activity of a mixed microbial culture, selected from a municipal landfill by its capability to grow in a water PU dispersion (WPUD) as the only carbon source, as a model for the BP8 landfill microbial community. The WPUD contains a polyether-polyurethane-acrylate (PE-PU-A) copolymer and xenobiotic additives (N-methylpyrrolidone, isopropanol and glycol ethers). To identify the changes that the BP8 microbial community culture generates to the WPUD additives and copolymer, we performed chemical and physical analyses of the biodegradation process during 25 days of cultivation. These analyses included Nuclear magnetic resonance, Fourier transform infrared spectroscopy, Thermogravimetry, Differential scanning calorimetry, Gel permeation chromatography, and Gas chromatography coupled to mass spectrometry techniques. Moreover, for revealing the BP8 community structure and its genetically encoded potential biodegradative capability we also performed a proximity ligation-based metagenomic analysis. The additives present in the WPUD were consumed early whereas the copolymer was cleaved throughout the 25-days of incubation. The analysis of the biodegradation process and the identified biodegradation products showed that BP8 cleaves esters, CC , and the recalcitrant aromatic urethanes and ether groups by hydrolytic and oxidative mechanisms, both in the soft and the hard segments of the copolymer. The proximity ligation-based metagenomic analysis allowed the reconstruction of five genomes, three of them from novel species. In the metagenome, Frontiers in Microbiology | www.frontiersin.org 1

γ-hydroxybutyric acid (GHB) causes retrograde amnesia in juveniles and young adults. Earlier, we have reported that in adolescent rat, GHB impairs the hidden platform task performance in the Morris water maze. In the present study, a classical fear conditioning paradigm was used to examine the effects of GHB on the acquisition of contextual conditioning, a hippocampus-dependent associative task, and cued tone conditioning, a hippocampus-independent task, in adolescent rats. Administration of GHB before the presentation of tone-shock pairings dose-dependently disrupted the acquisition of contextual conditioning with no effect on tone conditioning, when conditioned fear was measured 24 h later. Administering GHB prior to testing did not disrupt either contextual or tone conditioning. These results demonstrate that in the adolescent rat exposure to GHB preferentially disrupt hippocampal-dependent learning.

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations

The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified…

The gut microbiota benefits humans via short-chain fatty acid (SCFA) production from carbohydrate fermentation, and deficiency in SCFA production is associated with type 2 diabetes mellitus (T2DM). We conducted a randomized clinical study of specifically designed isoenergetic diets, together with fecal shotgun metagenomics, to show that a select group of SCFA-producing strains was promoted by dietary fibers and that most other potential producers were either diminished or unchanged in patients with T2DM. When the fiber-promoted SCFA producers were present in greater diversity and abundance, participants had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production. Promotion of these positive responders diminished producers of metabolically detrimental compounds such as indole and hydrogen sulfide. Targeted restoration of these SCFA producers may present a novel ecological approach for managing T2DM.

play a role in these events. may history of remote antenatal infection, as well as preterm birth, raising the possibility that the placental microbiome explored. In addition, the authors identified associations between the composition of the placental microbiome and a microbiome was most similar to that of the oral cavity, but the clinical implications of this finding remain to be different from those reported in other parts of the body, including the skin and urogenital tract. The placental consistent presence of a microbiome in placentas from healthy pregnancies. This microbiome was consistently Contrary to the prevailing idea of a ''sterile'' intrauterine environment, Aagaard and coauthors demonstrated the

The study of the human commensal micro-flora has recently regained the interest of the scientific community, particularly after the development of genomics and bio-informatics. The genes of the microbes found in the various different cavities of the human organism are collectively called the human microbiome (HM). This is a complex system, which is estimated to consist of approximately 1014 bacterial cells, thus being 10 times larger than the total of human cells. Almost 400−500 different types of microbes form the intestinal flora of the HM. The commensal bacteria in the gut microbiota interact with each other and with the host immune system, contributing to the homeostasis of the organism. The intestinal microbiome has been shown to differ among individuals of the same sex, between sexes and between individuals of different ages. Εach individual human can be characterized by his/her own intestinal microbial fingerprint, which may be useful in the future for individualized medicine. Alteration in the composition and function of the commensal gut  microbiota has been associated with complex diseases such as inflammatory bowel
diseases (IBD), colorectal cancer, allergies and obesity. Manipulation of the gut microbiota by fecal microbiota transplantation
is an effective and safe treatment of IBD and infection with C. difficile, but the use of pre- and pro-biotics
for the manipulation of microbiota should be reconsidered in the light of the new information now available. This is
a review of recent findings concerning the role of the enteric HM in the development of the immune system, and its
connection to gut-related and non-gastroenterological diseases.

Biologically synthesized silver nanoparticles (SNPs) are being widely using in the field of medicine. Extracellular biosynthesis of silver nanoparticles was carried out by using medicinal plant extracts for the reduction of aqueous silver ions in short period. The silver nanoparticles formation was confirmed by the colour change of plant extracts (SNPs) and further confirmed with the help of UV-Vis spectroscopy. These Phytosynthesized silver nanoparticles were tested for antibacterial and antifungal activities using disc diffusion method. The test cultures are Proteus, Pseudomonas, Klebsiella, Bacillus and E.coli species of bacteria and Aspergillus, Fusarium, Curvularia and Rhizopus species of fungal were used. The microbial property of silver nanoparticles was analyzed by measuring the inhibition zone. The silver nanoparticles synthesized from stem bark extracts of Boswellia and Shorea; and leaf extract of Svensonia. The SNPs synthesized from bark extracts of Boswellia ovalifoliolata and Shorea tumbuggaia showed toxic towards Klebsiella and Aspergillus; and Pseudomonas and Fusarium species respectively. Whereas the growth of Pseudomonas and Rhizopus species were inhibited maximum by the SNPs synthesized from leaf extract of Svensonia hyderobadensis, the results indicate that the silver nanoparticles may have an important advantage over conventional antibiotics.

Objective: The present work was to investigate the characteristics of the cheese produced by purified enzyme of native isolate Aspergillus flavus and was compared with commercial calf rennet powder. Methods: The effect of pH, coagulation temperature, CaCl2 and enzyme concentration on the rennet clotting properties of milk were assessed. The pH (4.0) showed the most important influence on rennet coagulation time, while coagulation temperature (40 oC), CaCl2 (10mM) concentration and enzyme concentration (1%) showed the highest contribution to predict the firmness of the gel when compared with commercial calf rennet powder. Results: The physical parameters such as colour, body, texture, appearance, flavour and aroma were enhanced in cheese obtained with microbial rennet in comparison with those made with commercial calf rennet. Conclusion: The milk clotting enzyme activity obtained in the present experiments with Aspergillus flavus are promising from the point of view of the development of a commercial process.

In this review we focus on the revision of the prebiotic concept in the context of the new metagenomic era. Functional metagenomic data provided by the Human Microbiome Project are revolutionizing the view of the symbiotic relationship between the intestinal microbiota and the human host. A deeper knowledge of the mechanisms that govern the dynamic interplay between diet, intestinal microbiota and host nutrition opens the way to better information on the prebiotic structure-function relationships, tailoring prebiotic formula into specific health attributes. On the other hand, functional genomic studies of the sourdough microbial communities allow to scan the environmental variability to identify novel metabolic traits for the biosynthesis of new potential prebiotic molecules. The integration of the functional analyses provided by the massive sequencing of bacterial genomes and metagenomes will allow the rational production of a desired prebiotic molecule with specific functional pro...

In recent years, with more and more attention given to the study of microorganisms in oil fields, molecular biology and biotechnology methodology has been applied prosperously. This article described the most commonly-used molecular biology techniques and related biotechnological advances in oil fields research at present, which are based mainly on 16s rRNA, such as 16S rRNA sequencing, denaturant gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), etc. The article also points out their advantages and disadvantages, respectively and introduces some of the micro-organisms, which are of largest concerns in the research.

Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio Currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and th...

Metagenomics may be defined as a study of uncultured microorganisms. It includes quicker, cheaper sequencing skill and by using metagenomic approach, we can able to sequence uncultured microbial samples from their environment directly are expanding and transforming our view of the microbial world. Purify meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic based research. This article gives an idea about some bioinformatic techniques for metagenomics

Current meta-omics developments provide a portal into the functional potential and activity of the intestinal microbiota. The comparative and functional meta-omics approaches have made it possible to get a molecular snap shot of microbial function at a certain time and place. To this end, metagenomics is a DNA-based approach, metatranscriptomics studies the total transcribed RNA, metaproteomics focuses on protein levels and metabolomics describes metabolic profiles. Notably, the metagenomic toolbox is rapidly expanding and has been instrumental in the generation of draft genome sequences of over 1000 human associated microorganisms as well as an astonishing 3.3 million unique microbial genes derived from the intestinal tract of over 100 European adults. Remarkably, it appeared that there are at least 3 clusters of co-occurring microbial species, termed enterotypes, that characterize the intestinal microbiota throughout various continents. The human intestinal microbial metagenome fu...

Cittadini nella società della conoscenza atti del convegno supplemento alla rivista quadrimestrale micron (N. 11 / Luglio 2009 ) di Arpa Umbria Agenzia regionale per la protezione ambientale Bonifica, recupero ambientale e sviluppo del territorio: esperienze a confronto sul fitorimedio atti del convegno supplemento alla rivista quadrimestrale micron (N. 22 / Agosto 2012 ) di Arpa Umbria Agenzia regionale per la protezione ambientale Direttore Svedo Piccioni Direttore responsabile Fabio Mariottini Segreteria di redazione Markos Charavgis Direzione e redazione Via Pievaiola San Sisto 06132 Perugia Tel. 075 515961 -Fax 075 51596235 www.arpa.umbria.it [email protected] Design Paolo Tramontana Fotografia ICP Milano Stampa Grafox, Perugia

After decades of research trials, poultry feed ingradients and formulations were very much streamlined. However oflate many of these hitherto employed poultry feed inputs are used in alternate sectors limiting their availability for poultry and the prices are increasing at alarming rate giving a lethal blow to the poultry industry.

Globally, there are concerning trends of waste generation as we progress towards a more developed society. India, the second most populous country, is on the edge of being the fifth largest economy in the world. In the last five decades, its metropolitanization has increased by approximately 10% and would further rise to 20% by 2026. The increasing urbanization and evolving lifestyles, food habits, and standards prompt such exponential expansion of robust waste.

Da poco più di una decina di anni gli scienziati sono in grado di studiare il mondo microbico finora inesplorato. Le comunità micro-biche che co-abitano dentro e attorno a noi esseri umani compongo-no il 'microbioma', che si è scoperto avere un grande impatto sia sulla nostra salute sia su quella dell'ambiente. Questo libro illustra come gli scienziati esplorano questo mondo microbico tra biologia, medicina e informatica, attraverso avanzate tecnologie di sequenziamento, big data e sistemi di intelligenza artificiale. Le pratiche di ricerca degli scienziati avvengono nella dialettica tra una 'visione molecolare' legata alla mappatura del genoma microbico-e una visione 'ecosistemica', dato che i microbi sono interdipendenti con l'ambiente e le sue dinamiche biosociali e culturali. In questo processo, biologia, medicina, informatica e antropologia si riconfigurano nel loro incontro e ciò porta a riconsiderare cosa significhi essere umani e il nostro ruolo in un mondo che esiste e persiste grazie, soprattutto, ai microbi.

The book illustrates how the microbiome paradigm opens up new understandings of health and of biology and how these are enacted by metagenomics researchers. Researchers are constrained by their onto-epistemic working practices but, at the same time, they take the microbiome ecosystem as an aspirational form of ecological co-habitation. Through the analysis of researchers’ lab practices, as well as of the features and frictions within their biographies and within the historical legacy of metagenomics, I sketch pathways for interdisciplinary collaboration between metagenomics and anthropology. Through a transdisciplinary reading of microbiome science practices, I also try to contribute to the critical (re)thinking of anthropology theory, method, and given-for-granted disciplinary assumptions.

Soil is a living entity of the Earth, and considered as one of the main reservoir of microbial diversity. Studying the soil microbial diversity is very much necessary, as they play an important role in maintaining the health of soil by recycling the nutrients, creating soil structure and humus. However, the culture dependent approaches fail to provide clear estimates of the diversity and untapped resources. Hence, study of the microbial diversity using culture independent approaches become necessary. The field of metagenomics helps in studying the genomes of the diverse soil organisms collectively in their natural habitat which holds the promising for accessing novel genetic resources. Application of the metagenomics to the soil environment is very challenging due to several difficulties; one of which is co-extraction of humic acid with nucleic acids which hinder downstream high throughout processes. However, applying sequencing methods to soil microbial communities will help in uncovering the hidden resources like novel genes, biomolecules and other valuable products which are yet to be discovered or still unknown. Different culture independent techniques and applications of the metagenomics to study the abundant microflora of the complex and changing environment of soil discussed herein.

Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring. We employed careful primer design and in vitro testing with mock communities to assess ability of the markers to amplify and sequence targeted species DNA, while retaining rank abundance information. In our mock communities, read abundances reflected the initial input abundance, with regressions having significant slopes (p<0.05) and high coefficients of determination (R 2) for all comparisons. Tests on field environmental samples revealed similar ability of our markers to measure relative abundance. Due to the limited reference sequence data available for these invertebrate species, care must be taken when analyzing results and identifying sequence reads to species level. These markers extend eDNA meta-barcoding research for molluscs and appear relevant to other invertebrate taxa, such as roti-fers and bryozoans. Furthermore, the sphaeriid mussel assay is group-specific, exclusively amplifying bivalves in the Sphaeridae family and providing species-level identification. Our assays provide useful tools for managers and conservation scientists, facilitating early detection of invasive species as well as improving resolution of mollusc diversity.

This study reviews the available molecular methods and new high-throughput technologies for their practical use in the molecular detection, quantification, and diversity assessment of microalgae. Molecular methods applied to other groups of organisms can be adopted for microalgal studies because they generally detect universal biomolecules, such as nucleic acids or proteins. These methods are primarily related to species detection and discrimination among various microalgae. Among current molecular methods, some molecular tools are highly valuable for small-scale detection [e.g., single-cell polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), and biosensors], whereas others are more useful for large-scale, high-throughput detection [e.g., terminal restriction length polymorphism, isothermal nucleic acid sequence-based amplification, loop-mediated isothermal amplification, microarray, and next generation sequencing (NGS) techniques]. Each molecular technique has its own strengths in detecting microalgae, but they may sometimes have limitations in terms of detection of other organisms. Among current technologies, qPCR may be considered the best method for molecular quantification of microalgae. Metagenomic microalgal diversity can easily be achieved by 454 pyrosequencing rather than by the clone library method. Current NGS, third and fourth generation technologies pave the way for the high-throughput detection and quantification of microalgal diversity, and have significant potential for future use in field monitoring.

Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host–symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.

Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of 44 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (B450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that 420% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.

To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. However, the great difficulty of quantifying biodiversity poses a serious roadblock to the development of effective policies to protect it. Metabarcoding technology can characterize the species compositions of mass samples of eukaryotes or environmental DNA. Here we validate metabarcoding as a means of biodiversity monitoring by testing it against three high-quality standard datasets collected in Malaysia (tropical), China (subtropical), and the UK (temperate), that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2505 person-hours of taxonomic expertise. We demonstrate that the metabarcode and standard datasets exhibit statistically correlated alpha- and beta-diversities, and we show that metabarcode and standard datasets produce similar policy conclusions for two conservation applications:  restoration ecology and systematic conservation planning. Compared with standard biodiversity datasets, which require individual identification of large numbers of specimens, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, lower-cost, less reliant on scarce taxonomic expertise, and auditable by third parties, which is essential for dispute resolution. These advantages increase the efficiency of large-scale surveillance of biodiversity trends and can alleviate many of the hidden-information problems that beset biodiversity-offset, environmental certification, and payment-for-environmental-service (PES) instruments.

Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome. Understanding plant microbiomes as a system allows analysis and integration of these complex interactions. Modern genomic studies involving metaomics and comparative studies can prove to be helpful in unraveling the gray areas of endophytism. A deeper knowledge of the mechanism of host infestation and role of endophytes could be exploited to improve the agricultural management in terms of plant growth promotion, biocontrol and bioremediation. Genome sequencing, comparative genomics, microarray, next gen sequencing, metagenomics, metatranscriptomics are some of the techniques that are being used or can be used to unravel plant–endophyte relationship. The modern techniques and approaches need to be explored to study endophytes and their putative role in host plant ecology. This review highlights " omics " tools that can be explored for understanding the role of endophytes in the plant microbiome.