16s rRNA Metagenomics

We aimed to determine the bacterial diversity of different oral micro-niches and to assess whether saliva and plaque samples are representative of oral microbial composition. We took minute samples from each surface of the individual teeth and gingival crevices of two healthy volunteers (112 samples per donor), as well as samples from the tongue dorsum and non-stimulated and stimulated saliva. DNA was extracted from 67 selected samples of each donor, and the 16S rRNA gene was amplified by PCR and pyrosequenced to obtain, on average, over 2,700 reads per sample, which were taxonomically assigned to obtain a geographic map of bacterial diversity at each tooth and sulcus location. Analysis of the data shows considerable differences in bacterial composition between teeth at different intra-oral locations and between surfaces of the same tooth. The most pronounced differences were observed in incisors and canines, where genera like Streptococcus were found at 40% to 70% on the vestibular surfaces but were almost absent on the lingual sides. Saliva samples, especially non-stimulated saliva, were not representative of supra-and subgingival plaque in the two individuals tested. We suggest that more precise sampling is required for the proper determination of oral microbial composition and to relate that diversity to epidemiological, clinical, and etiological parameters.

One sentence summary: This study gives insight into the bacterial community composition related to iron-cycling in suboxic marine sediments based on 16S rRNA gene pyrosequencing. ABSTRACT To gain insight into the bacterial communities involved in iron-(Fe) cycling under marine conditions, we analysed sediments with Fe-contents (0.5–1.5 wt %) from the suboxic zone at a marine site in the Skagerrak (SK) and a brackish site in the Bothnian Bay (BB) using 16S rRNA gene pyrosequencing. Several bacterial families, including Desulfobulbaceae, Desulfuromonadaceae and Pelobacteraceae and genera, including Desulfobacter and Geobacter, known to reduce Fe were detected and showed highest abundance near the Fe(III)/Fe(II) redox boundary. Additional genera with microorganisms capable of coupling fermentation to Fe-reduction, including Clostridium and Bacillus, were observed. Also, the Fe-oxidizing families Mariprofundaceae and Gallionellaceae occurred at the SK and BB sites, respectively, supporting Fe-cycling. In contrast, the sulphate (SO 4 2−) reducing bacteria Desulfococcus and Desulfobacterium were more abundant at greater depths concurring with a decrease in Fe-reducing activity. The communities revealed by pyrosequencing, thus, match the redox stratification indicated by the geochemistry, with the known Fe-reducers coinciding with the zone of Fe-reduction. Not the intensely studied model organisms, such as Geobacter spp., but rather versatile microorganisms, including sulphate reducers and possibly unknown groups appear to be important for Fe-reduction in these marine suboxic sediments.

Paenibacillus larvae is one of the major bacterial pathogens of honey bee broods and the causative agent of American foul-brood (AFB) disease. The factors responsible for the pathogenesis of AFB disease are still not fully understood, and the increasing resistance of P. larvae to commonly used antibiotics requires a search for new agents to control this disease. An in vitro screen was carried out to determine the antagonistic activity of gut bacteria isolated from indigenous honey bees, Apis mellifera jemenitica of Saudi Arabia against P. larvae. The gut bacterial isolates were evaluated individually against P. larvae ATCC9545 strain by the disc diffusion method. Seven of the 100 evaluated gut bacterial isolates, Fructobacillus fructosus (KY027123); Proteus mirabilis (KY027132); Bacillus licheniformis (KY027142); Lactobacillus kunkeei (KY027158); Bacillus subtilis (KY027169); Enterobacter kobei (KY027178); and Morganella morganii (KY027186) showed strong inhibitory effects. To our knowledge, this the first demonstration of antagonistic activity of F. fructosus, P. mirabilis, E. kobei, and M. morganii isolated from honey bee gut against P. larvae. The tested gut isolates exhibited significant antimicrobial activities against P. larvae, and they could play an important role in the treatment or prevention of AFB disease.

Interacting microbial communities flourishing in a healthy matrix or surviving in a monopolistic environment, as red meat. Colorectal cancer is just one of the issues tacked in this collection of international papers, but I wanna not to spoiler more with this digest and I let you undecode the following PCR-DGGE, HD-SPME-GS/MS, HTS Illumina sequencer, hence, awake of them, but not of the review.

The bioremediation process of industrial waste can be made more efficient using ligninolytic laccase enzymes, which are obtained from fungi, bacteria, higher plants, insects, and also in lichen. Laccase are catalyzed in the mono-electronic oxidation of a substrate from the expenditure of molecular oxygen. This enzyme belongs to the multicopper oxidases and participates in the cross linking of monomers, involved in the degradation of wide range industrial pollutants. In recent years, these enzymes have gained application in pulp and paper, textile and food industries. There are numerous reviews on laccases; however, a lot of information is still unknown due to their broad range of functions and applications. In this review, the bacterial laccases are focused for the bioremediation of various industrial pollutants. A brief description on structural molecular and physicochemical properties has been made. Moreover, the mechanism by which the reaction is catalyzed, the physical basis of thermostability and enantioselectivity, which requires more attention from researchers, and applications of laccase in various fields of biotechnology are pointed out. Environmental impact A bacterial laccase is a multi-copper oxidase and extracellular isozyme with a broad range of substrate specicity. It is mainly induced in industrial waste degradation for environmental safety. Its molecular and biochemical properties in the bacterial system is fragmentary and very little known in the literature because the bacterial cell is more versatile in its nutritional and environmental adaptation. Therefore, the knowledge role of laccase in bioremediation applications for various industrial wastes will open ample opportunities for large scale application through slight variation in the structural and functional properties of bacterial and fungal laccases. There are limitations for the large-scale application. Thus, this manuscript will support the researcher in understanding the thermo-tolerant mechanism and the application of this enzyme under alkaline conditions.

The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal mi-crobiota composition. The main differences were observed at the phylum level during the nursery phase, and the prevailing phyla were CKC4 (37.3%), Proteobacteria (29.8%), Actinobacteria (11.6%), and Firmicutes (10.1%). In the harvest phase, the prevailing phyla were Proteobacteria (28.4%), Chloroflexi (19.9%), and Actinobacteria (15.1%). At the ge-nus level, microbiota from the nursery phase showed greater relative abundances of CKC4 uncultured bacterium (37%) and Escherichia-Shigella (18%). On the contrary, in the microbiota of harvested shrimp, the prevailing genera were uncultured Caldilinea (19%) and Alphaproteobacteria with no other assigned rate (10%). The analysis of similarity ANOSIM test (beta diversity) indicated significant differences between the shrimp microbiota for these two farming phases. Similarly, alfa-diversity analysis (Chao1) indicated that the microbiota at harvest was far more diverse than the microbiota during the nursery phase, which showed a homogeneous composition. These results suggest that shrimp microbiota diversify their composition during intensive farming. The present work offers the most detailed description of the microbiota of P. vannamei under commercial production conditions to date.

The present work deals with the diversity and distribution of VAM fungi in soil samples of Kalaburagi district, Karanataka.
Kalaburagi is an important agriculture based district of Hyderabad Karnataka region in the state of Karnataka. The main crops of
the district are Cajanus cajan, Sorghum bicolar, Triticum aestivum, Saccharum officinalis etc. The soil samples were collected
from natural and artificial plantations, agricultural field and grassland during summer (March- June), monsoon (July-mid
October) and winter (mid October.-February) seasons. In artificial plantation, the lowest frequency of the spores were recorded in
all the three seasons. In natural plantation the maximum spore frequency was recorded in winter, while in agricultural fields and
grassland, the spore frequency showed gradual increase from summer through monsoon to winter. The studies were conducted to
record the diversity of VAM fungal spores in the different soil types at different seasons in agricultural soils of the district. The
higher number of spores were recorded from all the soil samples, collected in the month of November. The spore number was
found to be lowest in the month of August in all types of soil. Silt loam soil showed highest spore population, whereas the sandy
loam soil showed lowest spore population compared to others. The spore population density decreased in a descending order from
November to August in all types of agricultural soil of District. The Genus Glomus was well distributed in agricultural soils and
occupied > 50% of total VAM spore population present in all types of soil.

This study aimed at testing the efficacy and safety of Dacryodes edulis plant parts in diets fed to chicken. The plant has potential for use as a natural prebiotic to substitute the conventionally used antibiotic growth promoters in poultry production. Phytochemical analyses of the plant leaves, stem, and bark combination (stembark) and seed powders from the D. edu-lis were carried out. The powder from the three D. edulis plant parts were used as supplement in formulating six experimental diets tested in this study. The diets were TL 0Ed (0.5% leaves powder), TL 1Ed (1.0% leaves powder), TB 0Ed (0.5% stem-bark powder), TB 1Ed (1.0% stembark powder), TS 0Ed (0.5% seeds powder), and TS 1Ed (1.0% seeds powder). Besides, a positive (T + positive control; 0.5-g oxytetracycline as recommended by the manufacturer) and a negative (T-negative control ; having no commercial antibiotic and no plant supplement) diets were prepared for comparison purposes. The diets were fed to a total of 288 dual-purpose chicken for a period of 14 weeks. The chicken growth and body composition characteristics, blood chemistry, and micro-biota count were collected and used as indicators of the plant parts efficacy and safety. The analysis of the D. edulis plant parts significantly differed (P ≤ 0.05) in their phytochemical contents. The initial body weight and feed conversion efficiency ratios were not significantly different (P ≥ 0.05) between and among treatment groups. However, significant differences (P ≤ 0.05) were detected in the feed intake and body weight gain at eighth week. Live weight at eighth week was significantly different (P ≤ 0.05) with its values ranging between 503.32 and 614.93 g for treatments TL 1Ed and T Neg-, respectively. The dietary treatment of D. edulis leaves, stembark, and seed powder at the two inclusion levels significantly (P ≤ 0.05) decreased the colonies forming unit of Escherichia coli and Salmonella sp. as compared with negative control treatment in the eighth week phase. The level of glucose, total cholesterol, triglycer-ides, aspartate aminotransferase, alanine amino transferase, alkaline phosphatase, and the packed cell volume did not differ significantly (P ≥ 0.05) between and among dietary D. edulis treatments. The findings from this research provide crucial information on the efficacy and safety of D. edu-lis plant parts. This is an important step in testing the potential of the plant in use as a prebiotic in chicken feeds production.

Biofilm-forming marine bacterium Pseudomonas aeruginosa JP-11 was isolated from coastal marine sediment of Paradeep Port, Odisha, East Coast, India, which resisted up to 1,000 ppm of cadmium (Cd) as cadmium chloride in aerobic conditions with a minimal inhibitory concentration of 1,250 ppm. Biomass and extracellular polymeric substances (EPS) secreted by the cells effectively removed 58.760±10.62 and 29.544±8.02 % of Cd, respectively. The integrated density of the biofilm-EPS observed under fluores-cence microscope changed significantly (P≤0.05) in the presence of 50, 250, 450, 650 and 850 ppm Cd. ATR-FTIR spectroscopy showed a peak at 2,365.09/cm in the presence of 50, 250, 450 and 650 ppm Cd which depicts the presence of sulphydryl group (–SH) within the EPS, whereas, a peak shift to 2,314.837/cm in the presence of 850 ppm Cd suggested the major role of this functional group in the binding with cadmi-um. On exposure to Cd at 100, 500 and 1,000 ppm, the expression profiles of cadmium resistance gene (czcABC) in the isolate showed an up-regulation of 3.52-, 17-and 24-fold, respectively. On the other hand, down-regulation was observed with variation in the optimum pH (6) and salinity (20 g l −1) level. Thus, the cadmium resistance gene expression increases on Cd stress up to the tolerance level, but an optimum pH and salinity are the crucial factors for proper functioning of cadmium resistance gene.

Background

Jatropha curcas L. (Jatropha) is a potential biodiesel crop that can be cultivated on marginal land because of its strong tolerance to drought and low soil nutrient content. However, seed yield remains low. To enhance the commercial viability and green index of Jatropha biofuel, a systemic and coordinated approach must be adopted to improve seed oil and biomass productivity. Here, we present our investigations on the Jatropha-associated nitrogen-fixing bacteria with an aim to understand and exploit the unique biology of this plant from the perspective of plant–microbe interactions.

Results

An analysis of 1017 endophytic bacterial isolates derived from different parts of Jatropha revealed that diazotrophs were abundant and diversely distributed into five classes belonging to α, β, γ-Proteobacteria,Actinobacteria and Firmicutes.Methylobacterium species accounted for 69.1 % of endophytic bacterial isolates in leaves and surprisingly, 30.2 % which were able to fix nitrogen that inhabit in leaves. Among the Methylobacterium isolates, strain L2-4 was characterized in detail. Phylogenetically, strain L2-4 is closely related to M. radiotolerans and showed strong molybdenum-iron dependent acetylene reduction (AR) activity in vitro and in planta. Foliar spray of L2-4 led to successful colonization on both leaf surface and in internal tissues of systemic leaves and significantly improved plant height, leaf number, chlorophyll content and stem volume. Importantly, seed production was improved by 222.2 and 96.3 % in plants potted in sterilized and non-sterilized soil, respectively. Seed yield increase was associated with an increase in female–male flower ratio.

Conclusion

The ability of Methylobacterium to fix nitrogen and colonize leaf tissues serves as an important trait for Jatropha. This bacteria–plant interaction may significantly contribute to Jatropha’s tolerance to low soil nutrient content. Strain L2-4 opens a new possibility to improve plant’s nitrogen supply from the leaves and may be exploited to significantly improve the productivity and Green Index of Jatropha biofuel.

Electronic supplementary material

The online version of this article (doi:10.1186/s13068-015-0404-y) contains supplementary material, which is available to authorized users.

Keywords: Culturable endophyte, Nitrogen fixation, Methylobacterium, Jatropha curcas L., Biofuel

Acrobeloides maximus consistently comprised a set of different microorganisms compared to the microbiome of Caenorhabditis elegans or the metagenome of the soil sample to which nematodes were exposed. Using 16S rRNA gene amplification, the bacterial genera Ochrobactrum, Pedobacter, and Chitinophaga were identified at significant levels within the A. maximus communities only and were found to be consistently present during each of the three sampling periods over six months. We were able to isolate and grow colonies of Ochrobactrum and Pedobacter from the microbiome of the nematode on Lysogeny Broth-Miller (LB) and Yeast Extract (YE) agar plates. We were unable to isolate the associate from the genus Chitinophaga. The results obtained suggest a possible specific and persistent association between A. maximus and the two bacterial isolates we were able to culture.

With fluorescence in situ hybridization (FISH) with probes specific for Ochrobactrum and Pedobacter, we were able to stain these bacterial cells and show that they reside within the intestinal tract of A. maximus. It is possible that these gut bacteria may be mutualistic by providing A. maximus with essential metabolites, by aiding the nematode in the digestion of other bacteria, or by providing it with protection against pathogens.

Using 16S rRNA amplification and sequencing, three bacterial strains belonging to the genera Ochrobactrum, Pedobacter, and Chitinophaga were detected at significant levels within cultured Acrobeloides maximus populations exposed to soil for 24 hours before extraction and re-inoculation on agar. All three strains were found to persist in re-inoculated A. maximus cultures over a period of six months. For each strain, sequences from our A. maximus associated clones along with relevant 16S rRNA sequences from congeners or related genera available in GenBank were subjected to comprehensive phylogenetic analyses. Sequences were aligned using the multiple sequence alignment algorithms implemented in T-Coffee, MAFFT, Kalign, and WebPRANK, and phylogenetic trees were constructed using Bayesian and maximum-likelihood methods. Similarities and differences among the different alignment and tree-building methods suggest tree building methods with T-Coffee performed more poorly while maximum-likelihood methods with MAFFT and Kalign produced more mutually consistent topologies that correspond better to recognized genus boundaries. Inferences are made about the known species that are phylogenetically closest to each of our three strains. Our Ochrobactrum strains appear to be most closely related to Ochrobactrum tritici, while our Chitinophaga strains are most similar to a bacterium previously identified as “Flexibacter cf. sancti.” Our Pedobacter strains seem to be a previously undescribed sphingobacterium within the genus.

Serratia marcescens, a gram negative bacillus is generally related to hospital acquired infections. Production of red pigment (Prodiogisin) by the bacterium is an important characteristic feature and has been reported to exhibit certain antimicrobial property. The resistance of the bacteria towards several classes of antibiotics makes it one of the most notorious pathogen. The work aimed to evaluate the resistance of Serratia marcescens (SPKD15) under various environmental stress conditions (temperature, pH, Salt concentration and UV). Effect of these stress conditions on the cell viability and production of prodiogisin was analysed. The strain was able to sustain up to temperature of 40°C, Salt (NaCl) concentration of 7%, pH up to 10 and could withstand UV radiations up to 2 minutes. However, the prodiogisin production was negatively affected and finally inhibited at all the conditions of environmental stress(Temperature = 35°C, pH = 4 and 9, Nacl concentration = 4% and UV exposure of 15 seconds). This indicates that prodiogisin may act as a protective mechanism for the bacterium under stress. Further, intracellular antimicrobial was obtained from the UV exposed culture and compared with the antimicrobial obtained from the normal culture. The antimicrobial obtained from UV exposed culture showed decreased antimicrobial effect with inhibition diameter ranging between 2 mm to 13 mm (± S.D) as compared to the antimicrobial obtained from the normal culture. An inhibition diameter ranging between 4 mm to 22 mm (± S.D) was obtained in case of the normal culture which may be attributed to the loss of pigmentation. The study highlights the resistance of the bacterium to various environmental stresses. Keeping the degree of pathogenicity of the bacterium in mind, eradication of the same is quite difficult and must be looked upon seriously.

High-temperature environments (>70°C) contain diverse and abundant members of the crenarchaeal order Thermoproteales. However, a comprehensive study of the distribution and function of diverse members of this group across different habitat types has not been conducted. Consequently, the goals of this study were to determine the distribution of different Thermoproteales genera across geochemically distinct geothermal habitats of Yellowstone National Park, and to identify key functional attributes of major genera that correlate with environmental parameters. Curated sequence assemblies belonging to five genera were characterized in replicate samples of 11 high-temperature communities ranging in pH from 3 to 9. Thermocladium, Vulcanisaeta and Caldivirga spp. were the primary Thermoproteales populations present in low pH (pH < 5) habitats, whereas Thermoproteus populations were found in mildly-acidic (pH 5–6) sulfur sediments, and Pyrobaculum populations were confined to higher pH (pH>6) sulfur sediments and/or filamentous ‘streamer’ communities. Metabolic reconstruction and comparative genomics among assemblies show that these populations are primarily chemoorganotrophs that utilize different electron acceptors depending on geochemical conditions. The presence of potential CO2 fixation pathways in some Thermoproteales populations appears to be linked with NiFe hydrogenases, which combined with high levels
of H2 in many sulfidic systems, may provide the energy required to fix inorganic C.

Essential amino acids are important in aquatic animal growth rate. Hence, this study was carried out to find out
the enhancement of five selected essential amino acid namely tryptophan, lysine, methionine, valine and isoleucine
by carbon concentration and fermentation period in soy pulp for aquaculture uses. In the present study, fermentation
medium containing (soy pulp, 95.5%; yeast extract, 2%; ammonium sulphate, 2%; 0.5% glucose v/v) were subjected
to solid state fermentation for fermentation period screening (0 day, 4 days, 8 days, and 12 days) inoculated with
Bacillus cereus (MH027625). To acknowledge, the soy pulp, yeast extract and ammonium sulphate is in powder
form. Out of four fermentation periods, 8 days of fermentation was the best period of fermentation for maximum total
essential amino acid enhancement (42.9 ± 19.5 gL-1). This medium was further supplemented with different type
of carbon sources (glucose, sucrose, and molasses) at 0.5% v/v to increase total enhancement of essential amino
acid. The best carbon source (sucrose) was then further supplemented with different concentration (0%, 2%, 4%,
6%, 8%, and 10% v/v) to increase total enhancement of essential amino acid. Finally, total essential amino acids
were successfully enhanced with 43.1 ± 1.63 gL-1 of production after 8 days of fermentation supplemented with 2%
sucrose.

In many marine surface sediments, the reduction of manganese (Mn) and iron (Fe) oxides is obscured by sulfate reduction, which is regarded as the predominant anaerobic microbial respiration process. However, many dissimilatory sulfate and sulfur reducing microorganisms are known to utilize alternative electron acceptors such as metal oxides. In this study, we tested whether sulfate and sulfur reducing bacteria are linked to metal oxide reduction based on biogeochemical modeling of porewater concentration profiles of Mn2+ and Fe2+ in Bothnian Bay (BB) and Skagerrak (SK) sediments. Steady-state modeling of Fe2+ and Mn2+ porewater profiles revealed zones of net Fe (0–9 cm BB; ∼10 and 20 cm SK) and Mn (0–5 cm BB; 2–8 cm SK) species transformations. 16S rRNA pyrosequencing analysis of the in-situ community showed that Desulfobacteraceae, Desulfuromonadaceae and Desulfobulbaceae were present in the zone of Fe-reduction of both sediments. Rhodobacteraceae were also detected at high relative abundance in both sediments. BB sediments appeared to harbor a greater diversity of potential Fe-reducers compared to SK. Additionally, when the upper 10 cm of sediment from the SK was incubated with lepidocrocite and acetate, Desulfuromonas was the dominant bacteria. Real-time quantitative polymerase chain reaction (qPCR) results showed decreasing dsrA gene copy numbers with depth coincided with decreased Fe-reduction activity. Our results support the idea that sulfur and sulfate reducing bacteria contribute to Fe-reduction in the upper centimeters of both sediments.

Abstract
Antimicrobial resistance, especially the emergence of multidrug-resistant human pathogens, remains a serious public health crisis across the globe. The human gut microbiome regulates essential human functions including digestion, energy metabolism, brain function, and immunity by modulating multiple endocrine, neural, and immune pathways of the host. Increasing evidence shows adverse effects of antibiotics on the community structure and functions of healthy gut microbiomes. Short-term antibiotic treatment is able to change the richness and diversity of species into a long-term dysbiotic state. The colonization of invading pathogens is encouraged because of decreased competitive exclusion. Furthermore, the accumulation of antimicrobial resistant genes in the gut microbiome (gut resistome) facilitates the emergence of multidrug-resistant nosocomial pathogens. In this study, the adverse effects of antibiotics on the gut microbiome are highlighted in terms of dysbiosis and the accumulation of resistance genes. In light of evidence of such adverse impacts, several epidemiological studies have been conducted on traditional culture techniques and 16S rRNA metagenomics to assess the compositional and functional changes occurring in the gut microbiome after exposure to antibiotics. They have failed to agree on specific antibiotic-associated microbiome and its functional redundancy subsequent to exposure to antibiotics. This mini-review describes the composition and role of a healthy microbiome to understand and appraise the value of gut microbiome and summarizes the current understanding of adverse effects of antibiotics on it.
Keywords: Gastrointestinal Microbiome, Anti-bacterial Agents, Health
Citation: Perera M, Perera I. Fire in the forest: adverse effects of antibiotics on the healthy human gut microbiome. Int J Med Rev. 2018;5(1):19-26. doi:10.29252/IJMR-050104

Relationships between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses to resource pulses: growth increased with 16S rRNA gene copy number and declined with genome size after substrate addition to soils, responses that were repeated in four different ecosystems. Genome size best predicted growth rate in response to addition of glucose alone; adding ammonium with glucose weakened the relationship, and the relationship was absent in nutrient-replete pure cultures, consistent with the idea that reduced genome size is a mechanism of nutrient conservation. Our findings demonstrate that genomic traits of soil bacteria can map to their ecological performance in nature, but the mapping is poor under native soil conditions, where genomic traits related to stress tolerance may prove more predictive. These results remind that phenotype depends on environmental context, underscoring the importance of verifying proposed schemes of trait-based strategies through direct measurement of performance in nature, an important and currently missing foundation for translating microbial processes from genes to ecosystems.

Background Secondary symbionts of insects include a range of bacteria and fungi that perform various functional roles on their hosts, such as fitness, tolerance to heat stress, susceptibility to insecticides and effects on reproduction. These endosymbionts could have the potential to shape microbial communites and high potential to develop strategies for mosquito-borne disease control.

To date, it has been increasingly clear, that microbiota plays essential role in the host microorganism. Due to high phylogenetic diversity and wide distribution understanding of gut microbiota of fish is ambiguous. We elucidate previously undescribed diversity of bacteria in the White Sea fish posterior intestine based on 16S rRNA metabarcoding: shorthorn sculpin (Myoxocephalus scorpius), lumpfish (Cyclopterus lumpus) arctic flounder (Liopsetta glacialis), cod (Gadus morhua), and herring (Clupea pallasii). Proteobacteria were most abundant in all the samples. All datasets contained high number of reads corresponded to Psychrobacter, Halomonas, Pseudoalteromonas and Vibrio abundant in the White Sea water.Vast majority of bacterial reads corresponded to the Vibrionaceae (Aliivibrio, Vibrio, and Photobacterium). It is in accordance with our previous study focused on bioluminescent bacteria, where we isolated strains of these genera from the same fish intestine samples. The datasets of G. morhua and Cl. pallasii were enriched by reads of Shewanella (also isolated previously microbiologically due to luminescence of some its strains); the datasets of G. morhua and M. scorpius contained high number of Mycoplasma, which is in line with previous reports on the microbiome of marine fish gut from other geographical regions. Collectively, on the one hand, the study is a confirmation of known data on marine fish gut microbiome, on the other hand, it reveals some specific patterns of White Sea fish gut microbiota, e.g. presence of bacteria common for water from this region.

In a wide range of terrestrial ecosystems, different symbiotic mycorrhizal associations between plants and fungi occur, almost ubiquitously. Historically, these have chiefly been considered within the slightly narrow perspective of their effects on the uptake of dissolved mineral nutrients by distinct plants. Mycorrhizal fungi connect their plant hosts to the heterogeneously dispersed nutrients required for their growth, permitting the flow of energy-rich compounds required for nutrient mobilization whilst concurrently providing conduits for the translocation of mobilized products back to their hosts. In addition to growing the nutrient absorptive surface area of their host plant root systems, the extra radical mycelium of mycorrhizal fungi delivers a direct pathway for translocation of photosynthetically derived carbon to microsites in the soil and a huge surface area for interaction with other microorganisms. With phylogenetic surveys of soil ecosystems it has been known that the number of prokaryotic species in a single soil sample exceeds the known cultured prokaryotes. The soil environment is a plentiful yet under-characterized source of genetic diversity that has countless potential to enrich our understanding of soil microbial ecology and provide bioactive compounds and enzymes useful to human society. The complete functioning and regulation of these mycorrhizosphere processes is still poorly understood but current progress and the metagenomic studies are reviewed.

Chicken and eggs are an important source of protein for humans worldwide. Production of these foods has been intensified in recent years and around 150 million tonnes of chicken meat is expected to be produced by 2020 (OECD / FAO, 2018). However, one of the biggest problems linked to poultry production processes are the infectious diseases caused by pathogenic microorganisms. Among the most relevant are found microorganisms such as Salmonella ssp, Campylobacter spp, and Escherichia coli. Therefore, it is important to understand the mechanisms involved in the colonization of pathogenic microorganisms that can affect poultry and their interactions with the gastrointestinal microbiota, which are key in improving nutrient absorption and strengthening the immune system, which it influences the growth, welfare and health of the chicken. However, there is little information related to the gastrointestinal microbiota of chicken. Until recently, the characterization was limited to microorganisms that could be recovered through culture traditional. Therefore, in the last time, it has been intensified use of molecular techniques,  among those is remarked metagenomics, which offers an alternative for a better understanding of bacterial interactions, the identification of antibiotic resistance genes, identification of mobile genetic elements, and the design of strategies for more effective interventions with the aim of breaking the chain of transmission of pathogenic microorganisms during the poultry production cycle. In this review, the main metagenomics approaches are describe aimed to study microbiomes from poultry, sequencing techniques and bioinformatics tools used for its characterization.

Backgrounds: Landfill leachate is a complex composition containing high levels of ammonia nitrogen. Membrane bioreactor systems (MBRs) are used for this type of complex wastewater treatment, because of their capacity of working at high concentrations levels of suspended solids
and high cell retention times.
Objectives: In this study, 16S rRNA gene amplicon sequencing (NGS) combined with fluorescent in situ hybridization (FISH) were performed to identify detailed changes of nitrifying bacterial communities in activated sludge of two full-scale MBRs treating the waste effluents from
landfill leachate treatment systems.
Methods: Samples from activated sludge were collected monthly during fifteen months from two
MBR systems. The nitrifying bacterial communities were analyzed using 16S rRNA gene
amplicon sequencing (NGS) and fluorescence in situ hybridization (qFISH). Distance-based linear models (DISTLM) were applied to investigate models of environmental interpretation of
biological variables.
Conclusions: The two MBRs had different nitrifying microbial community compositions. In the MBR treating the waste effluents with high solids anaerobic digestion the ammonia oxidizing community was predominated by the family Nitrosomonadaceae y and the genus Nitrosococcus. In the MBR treating waste effluents with low solids the family Nitrosomonadaceae predominated but the genus Nitrosococcus was present a considerable lower abundances. We investigated
models of environmental interpretation of nitrifying variables using of distance-based linear models (DISTLM).

In the Anthropocene, humans, domesticated animals, wildlife, and their environments are interconnected, especially as humans advance further into wildlife habitats. Wildlife gut microbiomes play a vital role in host health. Changes to wildlife gut microbiomes due to anthropogenic disturbances, such as habitat fragmentation, can disrupt natural gut microbiota homeostasis and make animals vulnerable to infections that may become zoonotic. However, it remains unclear whether the disruption to wildlife gut microbiomes is caused by habitat fragmentation per se or the combination of habitat fragmentation with additional anthropogenic disturbances, such as contact with humans, domesticated animals, invasive species, and their pathogens. Here, we show that habitat fragmentation per se does not impact the gut microbiome of a generalist rodent species native to Central America, Tome's spiny rat Proechimys semispinosus, but additional anthropogenic disturbances do. Indeed, compared to protected continuous and fragmented forest landscapes that are largely untouched by other human activities, the gut microbiomes of spiny rats inhabiting humandisturbed fragmented landscapes revealed a reduced alpha diversity and a shifted and more dispersed beta diversity. Their microbiomes contained more taxa associated with domesticated animals and their potential pathogens, suggesting a shift in potential metagenome functions. On the one hand, the compositional shift could indicate a degree of gut microbial adaption known as metagenomic plasticity. On the other hand, the greater variation in community structure and reduced alpha diversity may signal a decline in beneficial microbial functions and illustrate that gut adaption may not catch up with anthropogenic disturbances, even in a generalist species with large phenotypic plasticity, with potentially harmful consequences to both wildlife and human health.

We redesigned an online non-majors General Biology course (Survey to Biosciences, BIO100) by implementing a
number of Constructivist and active learning approaches, and selecting a new textbook. Thirty courses before and
thirty courses after the redesign were analyzed for student survey results, BIO100 and the corresponding Survey to
Biosciences Laboratory (BIO100A) course grades, as well as the influence of student demographics such as age and
ethnicity. Official end-of-class surveys scores of student perceptions of teaching, learning, and course content were
compared pre- and post-redesign. We found that in the surveys only the perception of the textbook was significantly
improved after redesign. Additionally, no difference was found in survey scores between the thirteen instructors
teaching the course. No significant changes were found in either BIO100 or BIO100A grades after the redesign.
BIO100A grades were strongly associated with BIO100 grades. Strong relationships were found between certain
student demographic groups and BIO100A course grades, as well as between course enrollment and attrition

The marine environment, covering 70% of the planet’s surface, is estimated to contain 1030 viruses.
Despite their great importance in the marine environment, virtually very little is known about marine
viral biodiversity or the evolutionary relationships of marine and non-marine viruses. The present study
is aimed at molecular characterization and phylogenetic analysis of the viral Family Adenoviridae from
the marine environment, based on the hexon protein gene. Briefly, 50 L of sea water was purified and
concentrated by a combination of tangential flow filtration, flocculation and centrifugation.
Metagenomic DNA was extracted from the viral particles and PCR amplification was performed using
specific primers designed for hexon protein gene of adenoviruses. Positive amplicons were cloned and
sequenced. Sequences were analysed using GeneTool, BioEdit, ExPASy, ClustalW, GeneDoc and Mega
5.0 programmes. Partial hexon protein amplicon of 254 bp fragment encoding hexon protein of 84
amino acids could be recovered from the metagenomc viral DNA (KJ958986). Phylogenetic relationship
of the newly identified hexon protein gene was constructed employing neighbour joining method based
on already available hexon protein sequences in GenBank. The results of phylogenetic analysis
confirmed the basal placement of the newly identified hexon protein gene in the Adenoviridae family.
The present study shows that the newly identified adenovirus from marine environment is more closely
related to adenoviruses isolated from Ovine and Bovine sources than to other adenoviruses from
human sources. The present study provides a clearer insight into adenoviridae present in the marine

Background Mosquitoes are intermediate hosts for numerous disease causing organisms. Vector control is one of the most investigated strategy for the suppression of mosquito-borne diseases. Anopheles stephensi is one of the vectors of malaria parasite Plasmodium vivax. The parasite undergoes major developmental and maturation steps within the mosquito midgut and little is known about Anopheles-associated midgut microbiota.

Authors: Edward Alain B. Pajarillo, Jong Pyo Chae, Hyeun Bum Kim, In Ho Kim and Dae-Kyung Kang

The microbial communities in the pig gut perform a variety of beneficial functions. Along with host genetics and diet, farm management practices are an important aspect of agricultural animal production that could influence gut microbial diversity. In this study, we used barcoded pyrosequencing of the V1–V3 regions of the 16S ribosomal RNA (rRNA) genes to characterise the faecal microbiome of three common commercial purebred pig lines (Duroc, Landrace and Yorkshire) before and after cohabitation. The diversity of faecal microbiota was characterised by employing phylogenetic, distance-based and multivariate-clustering approaches. Bacterial diversity tended to become more uniform after mixing of the litters. Age-related shifts were also observed at various taxonomic levels, with an increase in the proportion of the phylum Firmicutes and a decrease in Bacteroidetes over time, regardless of the purebred group. Cohabitation had a detectable effect on the microbial shift among purebred pigs. We identified the bacterial genus Parasutterella as having utility in discriminating pigs according to time. Similarly, Dialister and Bacteroides can be used to differentiate the purebred lines used. The microbial communities of the three purebred pigs became more similar after cohabitation, but retained a certain degree of breed specificity, with the microbiota of Landrace and Yorkshire remaining distinct from that of their distant relative, Duroc.