scholarly journals Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Atsushi Kobiyama ◽  
Jonaira Rashid ◽  
Md. Shaheed Reza ◽  
Yuri Ikeda ◽  
Yuichiro Yamada ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Relative Abundance ◽  
Seawater Temperature ◽  
Community Diversity ◽  
Scaling Analysis ◽  
Dependent Manner ◽  
Low Diversity ◽  
Enclosed Bay ◽  
Positive Correlations ◽  
Domain Level

AbstractFive years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.

scholarly journals Early-Life Stress Modulates Gut Microbiota and Peripheral and Central Inflammation in a Sex-Dependent Manner

2021 ◽  
Vol 22 (4) ◽  
pp. 1899 ◽  
Author(s):  
Hae Jeong Park ◽  
Sang A. Kim ◽  
Won Sub Kang ◽  
Jong Woo Kim
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Life Stress ◽  
Early Life ◽  
Maternal Separation ◽  
Early Life Stress ◽  
Female Rats ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Male And Female Rats

Recent studies have reported that changes in gut microbiota composition could induce neuropsychiatric problems. In this study, we investigated alterations in gut microbiota induced by early-life stress (ELS) in rats subjected to maternal separation (MS; 6 h a day, postnatal days (PNDs) 1–21), along with changes in inflammatory cytokines and tryptophan-kynurenine (TRP-KYN) metabolism, and assessed the differences between sexes. High-throughput sequencing of the bacterial 16S rRNA gene showed that the relative abundance of the Bacteroides genus was increased and that of the Lachnospiraceae family was decreased in the feces of MS rats of both sexes (PND 56). By comparison, MS increased the relative abundance of the Streptococcus genus and decreased that of the Staphylococcus genus only in males, whereas the abundance of the Sporobacter genus was enhanced and that of the Mucispirillum genus was reduced by MS only in females. In addition, the levels of proinflammatory cytokines were increased in the colons (IFN-γ and IL-6) and sera (IL-1β) of the male MS rats, together with the elevation of the KYN/TRP ratio in the sera, but not in females. In the hippocampus, MS elevated the level of IL-1β and the KYN/TRP ratio in both male and female rats. These results indicate that MS induces peripheral and central inflammation and TRP-KYN metabolism in a sex-dependent manner, together with sex-specific changes in gut microbes.

PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 337-338
Author(s):  
Heather L Acuff ◽  
Tara N Gaire ◽  
Tyler Doerksen ◽  
Andrea Lu ◽  
Michael P Hays ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Fixed Effects ◽  
Mixed Model ◽  
Healthy Adult ◽  
Random Effect ◽  
Bacillus Coagulans ◽  
Community Diversity ◽  
Rrna Gene ◽  
Beagle Dogs ◽  
Fecal Microbiome

Abstract This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topical coating post-extrusion were randomly assigned to ten individually-housed Beagle dogs (7 castrated males, 3 spayed females) of similar age (5.75 ± 0.23 yr) and body weight (12.3 ± 1.5 kg) in a 5 x 5 replicated Latin square with 16-d adaptation and 5-d total fecal collection for each period. Five dietary treatments were formulated to deliver a dose of 0-, 6-, 7-, 8-, or 9-log10 CFU·dog-1·d-1. Fresh fecal samples (n=50) were analyzed by 16S rRNA gene pyrosequencing. Community diversity was evaluated in R (v4.0.3, R Core Team, 2019). Relative abundance data were analyzed using a mixed model (v9.4, SAS Institute, Inc., Cary, NC) with treatment and period as fixed effects and dog as a random effect. Results were considered significant at P < 0.05. Predominant phyla were Firmicutes (mean 81.2% ± 5), Actinobacteria (mean 9.9% ± 4.4), Bacteroidetes (mean 4.5% ± 1.7), Proteobacteria (mean 1.3% ± 0.7), and Fusobacteria (mean 1.1% ± 0.6). No evidence of shifts in predominant phyla, class, family, or genus taxonomic levels were observed except for the Bacillus genus, which had a greater relative abundance (P = 0.0189) in the low probiotic coating and high probiotic coating treatment groups compared to the extruded probiotic group. Alpha-diversity indices (Richness, Chao1, ACE, Shannon, Simpson, Inverse Simpson, and Fisher) and beta-diversity metrics (principal coordinate analysis and multi-dimensional scaling) were similar for all treatments. This data indicates that supplementation with Bacillus coagulans GBI-30, 6086 at a dose of up to 9 log10 CFU·d-1 did not alter the overall diversity of the fecal microbiome of healthy adult dogs over a 21-d period.

scholarly journals Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

2021 ◽  
Author(s):  
Ilan N. Rubin ◽  
Iaroslav Ispolatov ◽  
Michael Doebeli
Keyword(s):  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Metastable States ◽  
Community Diversity ◽  
Limited Resources ◽  
Niche Space ◽  
Stable States ◽  
Low Diversity ◽  
Population Sizes ◽  
Adaptive Radiations

AbstractOne of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur’s classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lokta-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.Author summaryUnderstanding if and when communities evolve to saturate their local environments is imperative to our understanding of natural populations. Using computer simulations of classical evolutionary models, we study whether adaptive radiations tend to lead toward saturated communities in which no new species can invade or remain trapped in alternative, lower diversity stable states. We show that with asymmetric competition and small effect mutations, evolutionary Red Queen dynamics can trap communities in low diversity metastable states. Moreover, limited resources not only reduces community population sizes, but also reduces community diversity, denying the formation of saturated communities and stabilizing low diversity, non-stationary evolutionary dynamics. Our results are directly relevant to the longstanding questions important to both ecological empiricists and theoreticians on the species packing and saturation of natural environments. Also, by showing the ease evolution can trap communities in low diversity metastable stats, we demonstrate the potential harm in relying solely on ESSs to answer questions of biodiversity.

Abstract MP51: Isolevuglandins In Antigen-presenting Cells, A Biomarker For Salt Sensitivity Of Blood Pressure In Humans?

Hypertension ◽  
2021 ◽  
Vol 78 (Suppl_1) ◽  
Author(s):  
Lale Ertuglu ◽  
Fernando Elijovich ◽  
Melis Sahinoz ◽  
Cheryl L Laffer ◽  
Ashley Pitzer ◽  
...  
Keyword(s):  
T Cell Activation ◽  
Cell Activation ◽  
Renal Medulla ◽  
Antigen Presenting Cells ◽  
Dependent Manner ◽  
Salt Loading ◽  
Elevation Changes ◽  
Salt Depletion ◽  
Positive Correlations ◽  
Antigen Presenting

Background: High Na+ stimulates antigen-presenting cells (APCs) in an ENaC dependent manner, with formation of isolevuglandin (isoLG) adducts (neoantigen peptides) that promote T cell activation and salt sensitive (SS) hypertension in rodents. Methods: We studied this pathway in 9 subjects with essential hypertension who discontinued anti-hypertensive therapy for 2 weeks. Their SS was assessed by 24-hrs of salt loading (460 mmoL) and salt depletion (10 mmoL/24 hr, plus furosemide 40 mg x 3). Muscle and skin Na + were measured at baseline (BA) by 23 Na magnetic resonance imaging (NaMRI). The % of APCs containing isoLG adducts (flow cytometry), urine and serum electrolytes and epoxyeicosatrienoic acids (EETs 8-9, 11-12 and 14-15) were measured at BA, after salt-loading (HI) and after salt-depletion (LO). Results: Age was 54 years (48-56), with 23% female, BMI 30 kg/m 2 (28-40) and screening SBP 136 mmHg (120-144), and DBP 85 mmHg (75-99). BA 24-hr urine Na + excretion was 178 (143-212) mmoL, Hi 392 (229-421) and LO 27 (25-29). SBP response to salt-depletion varied from -13.8 to +5.6 mmHg. Muscle Na+ correlated with duration of hypertension (r=0.73, p<0.03) and with SBP, DBP and mean arterial pressure (MAP) during BA, HI and LO (r=0.66 to 0.87). Mean %isoLGs in APCs were not different among the three stages of the protocol but ΔisoLGs due to HI or LO had positive correlations with ΔSBP, ΔDBP and ΔMAP produced by the same interventions (r=0.46 to 0.70). A 10% change in dendritic cell isoLGs predicted a 1.45 mmHg change of SBP in the same direction. Urine (not plasma) EETs (sum of three isoforms) showed negative correlations with isoLGs on the three phases of the protocol (r=0.57 to 0.69), and ΔEETs by HI and LO correlated negatively with ΔisoLGs produced by the same interventions (r=0.58 to 0.77). Conclusions: Muscle Na+ increases with duration of hypertension and correlates with severity of BP elevation. Changes in APC isoLGs due to Na+ loading or depletion seem to be a biomarker of SS of BP in humans. Relations between urine EETs and ΔEETs with APC isoLGs and ΔisoLGs suggest that EETs might be inhibitors of APC ENaC as they are of renal ENaC. Relationships between isoLGs and urine but not plasma EETs suggest that activation of APCs by high salt may occur in the hyperosmolar renal medulla.

scholarly journals Distribusi dan Kemelimpahan Meiofauna di Hulu Sungai Code Yogyakarta

2012 ◽  
Vol 9 (2) ◽  
pp. 34 ◽  
Author(s):  
Riche - Hariyati
Keyword(s):  
Dissolved Oxygen ◽  
Water Column ◽  
River Water ◽  
Relative Abundance ◽  
Horizontal Distribution ◽  
Water Current ◽  
Habitat Types ◽  
Chemical Parameter ◽  
Physico Chemical

This research is aimed to study distribution and abundance of meiofauna and the quality of physicochemicalcharacteristics of uppersite of code river and up stream river code Yogyakarta province. Samples weretaken using modified Pysto style corer and were located based on habitat types specific river, which are pool, riffle,rapid, left side and right side of water column. Sample taken four times for each zone. The parameter of for waterquality measured were dissolved oxygen. Water current, alkalinity and pHResult from the analysis showed that the abundance of meiofauna at code river the highest at left side zone.Which was 537.806 individu/m3 with relative abundance was 28,09% result from physico chemical parameter ofdissolved oxygenbetween 5,44 ppm – 6,0 ppm, alkalinity 20 ppm – 25 ppm , pH 7,10 – 7,18.and watercurrenntmeasured between 0,03 m/sec – 0,49 m/sec. The abundance of meiofauna at code river was dominated bygroup of Nematodes horizontal distribution of the fauna was the widest for Nematodes ostracoda, Rhizopoda andinsecta. Physico chemicalquality of code river water was relative good for meiofauna habitat and other waterorganisms

scholarly journals Herpes Simplex Virus Infection Stabilizes Cellular IEX-1 mRNA

2005 ◽  
Vol 79 (7) ◽  
pp. 4090-4098 ◽  
Author(s):  
Wei-Li Hsu ◽  
Holly A. Saffran ◽  
James R. Smiley
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Relative Abundance ◽  
Dependent Manner ◽  
Experimental Conditions ◽  
Viral Mrnas ◽  
Necrosis Factor Alpha ◽  
Translational Initiation ◽  
Simplex Virus ◽  
Hsv 1

ABSTRACT Herpes simplex virus (HSV) virion host shutoff protein (vhs) destabilizes cellular and viral mRNAs. Previous work from several laboratories has indicated that vhs accelerates the turnover of most host mRNAs and provided evidence that at least some of these are degraded via endonucleolytic cleavage near regions of translational initiation followed by 5′→3′ decay. In contrast, several recent reports have argued that vhs is selective, preferentially targeting a subset of mRNAs including some that bear AU-rich instability elements (such as the stress-inducible IEX-1 mRNA). These reports concluded that vhs triggers deadenylation, 3′ cleavage, and 3′→5′ decay of IEX-1 mRNA. However, we report here that HSV infection does not increase the rate of degradation of IEX-1 mRNA; rather, actinomycin D chase assays indicate that the transcript is stabilized relative to that in uninfected cells in both the presence and absence of functional vhs. Moreover, deadenylated but otherwise intact IEX-1 mRNA was readily detected in uninfected cells cultured under our experimental conditions, and its relative abundance did not increase following HSV type 1 (HSV-1) infection. We confirm that HSV infection increases the relative abundance of a discrete 0.75-kb 3′-truncated IEX-1 RNA species in a vhs-dependent manner. This truncated transcript was also detected (albeit at lower levels) in cells infected with vhs mutants and in uninfected cells, where it increased in abundance in response to tumor necrosis factor alpha, cycloheximide, and puromycin. We conclude that IEX-1 mRNA is not preferentially degraded during HSV-1 infection and that HSV-1 instead inhibits the normal turnover of this mRNA.

scholarly journals Analysis of the tonsillar microbiome in young adults with sore throat reveals a high relative abundance of Fusobacterium necrophorum with low diversity

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0189423 ◽  
Author(s):  
T. Prescott Atkinson ◽  
Robert M. Centor ◽  
Li Xiao ◽  
Fuchenchu Wang ◽  
Xiangqin Cui ◽  
...  
Keyword(s):  
Young Adults ◽  
Sore Throat ◽  
Relative Abundance ◽  
Fusobacterium Necrophorum ◽  
Low Diversity

Timing, cause and consequences of mid-Holocene climate transition in the Arabian Sea

2016 ◽  
Vol 86 (2) ◽  
pp. 162-169 ◽  
Author(s):  
Rajeev Saraswat ◽  
Dinesh Kumar Naik ◽  
Rajiv Nigam ◽  
Anuruddh Singh Gaur
Keyword(s):  
Dissolved Oxygen ◽  
Arabian Sea ◽  
Seawater Temperature ◽  
Subsurface Water ◽  
Water Interface ◽  
Holocene Climate ◽  
Carbon Burial ◽  
Sediment Fraction ◽  
Surface Productivity ◽  
Climate Transition

AbstractWe reconstruct centennial scale quantitative changes in surface seawater temperature (SST), evaporation-precipitation (from Mg/Ca and δ18O of surface dwelling planktic foraminifera), productivity (from relative abundance of Globigerina bulloides), carbon burial (from %CaCO3 and organic carbon [%Corg]) and dissolved oxygen at sediment-water interface, covering the entire Holocene, from a core collected from the eastern Arabian Sea. From the multi-proxy record, we define the timing, consequences and possible causes of the mid-Holocene climate transition (MHCT). A distinct shift in evaporation-precipitation (E-P) is observed at 6.4 ka, accompanied by a net cooling of SST. The shift in SST and E-P is synchronous with a change in surface productivity. A concurrent decrease is also noted in both the planktic foraminiferal abundance and coarse sediment fraction. A shift in carbon burial, as inferred from both the %CaCO3 and %Corg, coincides with a change in surface productivity. A simultaneous decrease in dissolved oxygen at the sediment-water interface, suggests that changes affected both the surface and subsurface water. A similar concomitant change is also observed in other cores from the Arabian Sea as well as terrestrial records, suggesting a widespread regional MHCT. The MHCT coincides with decreasing low-latitude summer insolation, perturbations in total solar intensity and an increase in atmospheric CO2.

scholarly journals Hypoxic conditions alter developing branchial arch-derived structures in zebrafish

2014 ◽  
Vol 2 (1) ◽  
Author(s):  
Trish E Parsons ◽  
Seth M Weinberg ◽  
Michael Tsang ◽  
Alexandre R Vieira
Keyword(s):  
Dissolved Oxygen ◽  
Cleft Lip ◽  
Branchial Arch ◽  
Hypoxic Exposure ◽  
Dependent Manner ◽  
Shape Variation ◽  
Zebrafish Model ◽  
Geometric Morphometric ◽  
Hypoxic Conditions ◽  
Hypoxia Group

Background: Previous epidemiological findings have implicated hypoxia as a risk factor for craniofacial defects including cleft lip, microtia and branchial arch anomalies. This study tests the hypothesis that hypoxic exposure results in craniofacial shape variation in a zebrafish model. Methods: Three sets of zebrafish embryos were raised in uniform conditions with the exception of dissolved oxygen level.  At 24 hours past fertilization (hpf) embryos were placed in hypoxic conditions (70% or 50% dissolved oxygen tank water) and compared to unexposed control embryos.  After 24 hours of exposure to hypoxia, the embryos were incubated under normoxia.  Larvae were collected at 5 days post fertilization (dpf) and stained for cartilage. Images were taken of each specimen and subsequently landmarked to capture viscerocranial morphology.  A geometric morphometric analysis was performed to compare shape variation across groups. Results: The mean branchial arch shape of each exposure group was significantly different from controls (p<0.001).  Principal components analysis revealed a clear separation of the three groups, with controls at one end of the shape spectrum, the 50% hypoxia group at the other end, and the 70% hypoxia group spanning the variation in between. Conclusions: This experiment shows that hypoxia exposure at 24hpf is capable of affecting craniofacial shape in a dose-dependent manner.  These results may have implications not only for high altitude fetal health, but other environments, behaviors and genes that affect fetal oxygen delivery. 

scholarly journals Profile of microbial community of organic and conventional rice field using metagenomic analysis

2021 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Arum Asri Trisnastuti ◽  
Edi Purwanto ◽  
Ari Susilowati
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Rice Field ◽  
Fertilizer Application ◽  
Rice Fields ◽  
Community Diversity ◽  
Total N ◽  
Organic C ◽  
Organic Rice ◽  
Significant Difference

Organic farming can increase the diversity of soil bacterial. This research aimed to compare the profile of microbial community of organic and conventional rice fields in early (0 Day After Planting/DAP), mid (15 DAP), and late (45 DAP) fertilizer application period. The total DNA genome from the soil sample was extracted then analyzed metagenomically using Next Generation Sequencing (NGS). There was nine genus of bacteria found in high relative abundance, 95.28%, while 4.72% included in Domain of Archaea (genus Methanosaeta). Phylum of Firmicutes (genus Clostridium has 24.50% relative abundance, Bacillus 11.90%, Lactobacillus 9.69%); Proteobacteria (genus Defluviicoccus 12.10%, Buchnera 18.46%, Rosenbergiella 2.46%); and Actinobacteria (genus Nocardioides 12.21%, and Streptomyces 3.96%). Meanwhile, the average plant height of organic rice fields was shorter than conventional rice fields got directly measured coincided with soil sampled. Based on alpha and beta diversity analysis, the highest community diversity and abundance were found in organic rice field soil samples taken at 45 DAP, i.e., at the end of the fertilizer application period. However, in both organic and conventional rice field soils, there was almost no significant difference in the bacterial community, so it impacts that organic and conventional systems do not make a real difference in the total N, P available, CEC, and pH values. It makes a significant difference in organic C and organic matters.

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