Changes In Relative Abundance Research Articles

Trout Responses to Stocking Rates and River Discharge within a Southeastern U.S. Hydropeaking Tailwater

AbstractFreshwater fish populations often exist in systems characterized by novel ecological processes resulting from human alteration. Salmonid populations embedded within coldwater sections of warmwater rivers are spatially constrained by habitat availability. Tailwater fish contend with fluctuating river discharges and density‐dependent processes associated with fish stocking and exploitation. Salmonid populations sustained through stocking versus natural reproduction may respond differently to changes in hydrologic patterns (e.g., hydropeaking) as well as declines in fish abundance. We assessed differences between stocked (Rainbow Trout Oncorhynchus mykiss) and naturalized (Brown Trout Salmo trutta) trout populations in Greers Ferry tailwater, Arkansas, regarding (1) spatial and temporal patterns of mean length, electrofishing catch rates, and relative condition following reduced number of stocked Rainbow Trout and (2) evidence that hydrologic characteristics and fish stocking intensity influenced relative condition. A 56% reduction in Rainbow Trout stocking did not result in systemwide change in mean length or relative abundance for Rainbow Trout or Brown Trout over the 16‐year study period. Hydrologic variability, where river discharge spanned both reduced and elevated levels, positively influenced condition of both Rainbow Trout and Brown Trout. Assessment of survival of stocked Rainbow Trout may aid in further refining the timing and amount of stocking needed to sustain the population at a desired abundance. Further, assessing the influence of stocking fewer but perhaps larger (in terms of mean length) fish to meet management goals may be warranted. The persistent differences in relative abundance among river sections can inform management actions directed at Brown Trout, including harvest regulations. Such regulations may aid in reaching desired management goals, including abundance and mean length targets not observed after reduced stocking.

Relative species abundance and population densities of the past: developing multispecies occupancy models for fossil data

AbstractThe number of individuals of species varies, but estimating abundance, given incomplete and biased sampling in both contemporary and fossilized communities, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, in which multispecies occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modeling framework is suited for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modeling framework using a fossil community of benthic organisms to estimate relative species abundance dynamics and changing relative population densities of focal species in nine (geological) time intervals over 2.3 Myr. We also explore potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time intervals. The modeling framework is applicable across a wide range of questions on species-level dynamics in paleoecological community settings.

Watershed-scale liming reveals the short- and long-term effects of pH on the forest soil microbiome and carbon cycling.

Soil microbial community composition routinely correlates with pH, reflecting both direct pH effects on microbial physiology and long-term biogeochemical feedbacks. We used two watershed-scale liming experiments to identify short- (2 years) and long-term (25 years) changes in the structure and function of bacterial and fungal communities in organic horizons (Oe and Oa ) of acid forest soils. Liming increased soil pH, extractable calcium, and soil carbon stocks, reduced biomass-specific respiration, and caused major changes in the soil microbiome in the short and long term. More taxa responded to liming in the short term (70%) than in the long term (30%), with most showing consistent directional responses at both sites. The ratio of change in relative abundance between limed and reference sites was twofold higher at the long than the short-term site, indicating that the effects of liming grew over time. Liming impacts were most pronounced in fungi, as steep declines of dominant ectomycorrhizal fungi (Cenococcum and Russula) occurred at both sites. Liming favoured neutrophilic bacteria over acidophilic populations according to estimated environmental pH optima. Collectively, these results demonstrate that a liming-induced change of one pH unit has an immediate and persistent effect on the structure and function of microbial communities in acid forest soils. The corresponding suppression of respiration indicates that anthropogenic alterations of soil pH, as driven by acid deposition or liming, can affect forest floor C stocks due to pH-driven shifts in community structure.

Influence of Microplastics on Microbial Structure, Function, and Mechanical Properties of Stream Periphyton

Periphyton is a freshwater biofilm composed of prokaryotic and eukaryotic communities that occupy rocks and sediments, forming the base of the food web and playing a key role in nutrient cycling. Given the large surface that periphyton comprises, it may also act as a sink for a diverse range of man-made pollutants, including microplastics (MP). Here we investigated the effect of 1–4 μm and 63–75 µm sized, spherical polyethylene MP with native and ultraviolet (UV)-weathered surface on developing natural stream periphyton communities over 28 days. In order to ensure proper particle exposure, we first tested MP suspension in water or in water containing either Tween 80, extracellular polymeric substances – EPS, fulvic acids, or protein. We found the extract of EPS from natural periphyton to be most suitable to create MP suspensions in preparation of exposure. Upon exposure, all tested types of MP were found to be associated with the periphyton, independent of their size and other properties. While biomass accrual and phenotypic community structure of the photoautotrophs remained unchanged, the prokaryotic and eukaryotic communities experienced a significant change in composition and relative abundances. Moreover, alpha diversity was affected in eukaryotes, but not in prokaryotes. The observed changes were more prominent in periphyton exposed to UV-treated as compared with native surface MP. Mechanical properties, as assessed by compression rheology, showed that MP-exposed periphyton had longer filamentous streamers, higher stiffness, lower force recovery and a higher viscoelasticity than control periphyton. Despite the observed structural and mechanical changes of periphyton, functional parameters (i.e., photosynthetic yield, respiration and nutrient uptake efficiencies) were not altered by MP, indicating the absence of MP toxicity, and suggesting functional redundancy in the communities. Together, our results provide further proof that periphyton is a sink for MP and demonstrate that MP can impact local microbial community composition and mechanical properties of the biofilms. Consequences of these findings might be a change in dislodgement behavior of periphyton, a propagation through the food chains and impacts on nutrient cycling and energy transfer. Hence, taking the omnipresence, high persistence and material and size diversity of MP in the aquatic environment into account, their ecological consequences need further investigation.

Responses of soil fungal taxonomic attributes and enzyme activities to copper and cadmium co-contamination in paddy soils

Excess heavy metals, especially copper (Cu) and cadmium (Cd), are common in paddy soils in the red soil hilly areas of southern China. Microorganisms are regulators of soil organic matter accumulation and pollutant transformation. Clarifying the effects of Cu and Cd accumulation on microbial community composition and function is a prerequisite for bioremediation of paddy soil contamination. However, it remains unclear how Cu and Cd contamination affects soil fungal taxonomic attributes and microbial-mediated biogeochemical processes in paddy soils. Here, soil heavy metals, fungal community composition, and soil enzyme activities were determined in paddy fields downstream of a typical mining area in southern China, and the effects of Cu and Cd co-contamination on fungal community diversity and co-occurrence networks, as well as the associations between them were assessed. The concentrations of Cu and Cd in paddy soils decreased from upstream to downstream of the river, and were positively correlated with the Shannon index of fungal communities. Soil Cu and Cd concentrations exhibited a greater impact on the structure and assembly of fungal communities than soil general properties. Increases in soil Cu and Cd concentrations were correlated with drastic changes in the cumulative relative abundance of ecological clusters in fungal co-occurrence networks. Soil Cu and Cd concentrations were positively correlated with the relative abundances of Eurotiomycetes, Pezizomycetes, Ustilaginomycetes, and Kickxellomycetes, respectively, whereas negatively correlated with hydrolase activities related to carbon, nitrogen, and phosphorus cycles. These results confirmed in the field that long-term Cu and Cd enrichment significantly altered the structure and diversity of fungal communities in the subtropical paddy soils, thereby affecting soil nutrient transformation and organic matter accumulation. This can also provide a basis for the bioremediation of heavy metal pollution in paddy soils.

High-throughput imaging of mRNA at the single-cell level in human primary immune cells.

Measurement of gene expression at the single-cell level has advanced the study of transcriptional regulation programs in healthy and disease states. In particular, single-cell approaches have shed light on the high level of transcriptional heterogeneity of individual cells, both at baseline and in response to experimental or environmental perturbations. We have developed a method for high-content imaging (HCI)-based quantification of relative changes in transcript abundance at the single-cell level in human primary immune cells and have validated its performance under multiple experimental conditions to demonstrate its general applicability. This method, named hcHCR, combines the sensitivity of the hybridization chain reaction (HCR) for the visualization of RNA in single cells, with the speed, scalability, and reproducibility of HCI. We first tested eight cell attachment substrates for short-term culture of primary human B cells, T cells, monocytes, or neutrophils. We then miniaturized HCR in 384-well format and documented the ability of the method to detect changes in transcript abundance at the single-cell level in thousands of cells for each experimental condition by HCI. Furthermore, we demonstrated the feasibility of multiplexing gene expression measurements by simultaneously assaying the abundance of three transcripts per cell at baseline and in response to an experimental stimulus. Finally, we tested the robustness of the assay to technical and biological variation. We anticipate that hcHCR will be suitable for low- to medium-throughput chemical or functional genomics screens in primary human cells, with the possibility of performing screens on cells obtained from patients with a specific disease.

Post-translational modifications to hemidesmosomes in human airway epithelial cells following diacetyl exposure

Diacetyl (DA; 2,3-butanedione) is a highly reactive alpha (α)-diketone. Inhalation exposure to DA can cause significant airway epithelial cell injury, however, the mechanisms of toxicity remain poorly understood. The purpose of these experiments was to assess for changes in abundance and distribution of hemidesmosome-associated proteins following DA exposure that contribute to DA-induced epithelial toxicity. Human bronchial epithelial cells were grown in submerged cultures and exposed to three occupationally-relevant concentrations of DA (5.7, 8.6, or 11.4 mM) for 1 h. Following DA exposure, epithelial cells were cultured for 4 days to monitor for cell viability by MTT and WST-1 assays as well as for changes in cellular distribution and relative abundance of multiple hemidesmosome-associated proteins, including keratin 5 (KRT5), plectin (PLEC), integrin alpha 6 (ITGα6) and integrin beta 4 (ITGβ4). Significant toxicity developed in airway epithelial cells exposed to DA at concentrations ≥ 8.6 mM. DA exposure resulted in post-translational modifications to hemidesmosome-associated proteins with KRT5 crosslinking and ITGβ4 cleavage. Following DA exposure at 5.7 mM, these post-translational modifications to KRT5 resolved with time. Conversely, at DA concentrations ≥ 8.6 mM, modifications to KRT5 persisted in culture with decreased total abundance and perinuclear aggregation of hemidesmosome-associated proteins. Significant post-translational modifications to hemidesmosome-associated proteins develop in airway epithelial cells exposed to DA. At DA concentrations ≥ 8.6 mM, these hemidesmosome modifications persist in culture. Future work targeting hemidesmosome-associated protein modifications may prevent the development of lung disease following DA exposure.

Pigs and polities in Iron Age and Roman Anatolia: An interregional zooarchaeological analysis

Anatolia witnessed an increase in mobility and interaction during the Iron Age. Peoples from Southeastern Europe and Southwest Asia migrated into and across Anatolia. At the same time, under the influence of expanding and competing polities, trade and military mobility reinforced supra-regional networks across land and sea. Little is known about how animal husbandry practices in Iron Age Anatolia changed in the face of these large-scale movements of people and goods. Especially little understood remains how past mobility and connectivity influenced pig husbandry, as pigs are generally considered rather immobile animals, and Iron Age animal mobility studies tend to focus on pastoralist practices (e.g. Hammer and Arbuckle, 2017). Yet, pig husbandry practices are highly plastic, and may have changed dynamically along with evolving economic and socio-cultural circumstances during the first millennium BC. In addition, palaeogenetic studies provide evidence that durign the Iron Age pigs with European lineages appeared and subsequently spread over Anatolia (Ottoni et al., 2013) suggesting pigs may have been actively incorporated in trade and mobility. Building on these two observations, this paper explores pig husbandry practices over the course of the Anatolian Iron Age (1200–600 BCE) by (1) discussing diachronic change in relative abundance of pigs and mortality patterns over different sites in first millennium BC Anatolia; (2) investigating whether the introduction of European pigs in Anatolia coincided with noticeable phenotypic changes in pig populations by looking at pig biometry using the R package zoolog. Primary data from various key sites are presented (Troy, Klazomenai, Gordion, Kerkenes, Kinet Höyük) alongside a meta-analysis of published zooarchaeological data.

Evaluating the impact of perioperative antibiotic prophylaxis on the microbiome in patients with cutaneous malignancy.

TPS9602 Background: Preoperative antibiotic prophylaxis is commonly used to reduce surgical site infections (SSIs). However, the rate of SSIs following surgical procedures classified as clean is only 2-3%. Overuse of antibiotics is associated with several potential adverse effects, including dysregulation of the gut microbiome. Disruption of the composition and function of the native gut microbiota, referred to as dysbiosis, has been implicated in a number of inflammatory and autoimmune disorders, as well as gastrointestinal (GI) and non-GI cancers. Recent studies have demonstrated that antibiotics have a profound and persistent effect on the gut microbiota, as evidenced by diminished overall abundance and diversity, as well as alteration of community composition that includes a decreased relative abundance of bacteria in the Ruminococcaceae family. In melanoma, diversity of gut microbiota and relative abundance of Ruminococaceae have been linked to improved survival and enhanced response following immune checkpoint blockade. In this study, we seek to determine the impact of preoperative prophylactic antibiotic use on the gut microbiome in patients following surgery for stage I or II melanoma. Methods: In this non-comparative randomized pilot trial, the impact of prophylactic antibiotic use at the time of surgical intervention on gut microbiome diversity and composition will be studied. Patients diagnosed with clinical stage I or II melanoma undergoing wide excision with or without lymphatic mapping and sentinel lymph node biopsy are randomized 1:1 to either receive preoperative cefazolin or no preoperative antibiotics. Stool samples and peripheral blood are collected before surgery, the day of surgery (optional), on post-operative day 3 (optional), and 2 weeks and 3 months following surgery. The primary endpoint for the study is change in microbiome alpha diversity at 2 weeks following surgery. Secondary endpoints are change in relative abundance of microbes at 2 weeks and 3 months after surgery and SSI rates according to whether or not prophylactic antibiotics were administered at time of surgery. Exclusion criteria include recent antibiotic use (within 3 months), allergy to beta-lactam or cephalosporin antibiotics, increased risk of infection due to medical comorbidity or use of immunosuppressive medication. Enrollment began in October 2021. As of January 2022, 22 of 30 patients have been accrued to ensure complete sample collection for 20 patients. Study findings may inform a larger trial evaluating interventions to mitigate antibiotic impact. Clinical trial information: NCT04875728.

Impact of Food-Based Weight Loss Interventions on Gut Microbiome in Individuals with Obesity: A Systematic Review.

The observation that the gut microbiota is different in healthy weight as compared with the obese state has sparked interest in the possible modulation of the microbiota in response to weight change. This systematic review investigates the effect of food-based weight loss diets on microbiota outcomes (α-diversity, β-diversity, relative bacterial abundance, and faecal short-chain fatty acids, SCFAs) in individuals without medical comorbidities who have successfully lost weight. Nineteen studies were included using the keywords ‘obesity’, ‘weight loss’, ‘microbiota’, and related terms. Across all 28 diet intervention arms, there were minimal changes in α- and β-diversity and faecal SCFA concentrations following weight loss. Changes in relative bacterial abundance at the phylum and genus level were inconsistent across studies. Further research with larger sample sizes, detailed dietary reporting, and consistent microbiota analysis techniques are needed to further our understanding of the effect of diet-induced weight loss on the gut microbiota.

Global metagenomics analyses demonstrate metformin‐induced changes in the gut mycobiome in subjects with type 2 diabetes

The fungal component of the gut microbiota (mycobiome) has been less well studied than bacterial populations; however, emerging evidence suggests that the mycobiome might play an important role in metabolic disease. Intestinal fungi play an important role in modulating immune responses at mucosal and systemic sites, but the extent of host‐bacterial‐fungi interactions in disease pathogenesis remains unknown. Metabolic diseases such as obesity and type 2 diabetes are accompanied by an altered gut microbiome, known as dysbiosis, and recent work suggests that the gut mycobiome may also be perturbed in metabolic diseases. Correcting gut dysbiosis is hypothesized as a therapeutic target for obesity and some metabolic diseases, however, little data is available regarding the effects of medications on the gut mycobiome and associated host‐bacterial‐fungi interactions. Metformin is globally the most prescribed drug for type 2 diabetes mellitus (T2D), and its therapeutic effects cause decreased hepatic gluconeogenesis and consequently circulating blood glucose. Metformin treatment also impacts the gut microbiome composition, lowering circulating lipopolysaccharide and therefore reducing toll‐like‐receptor‐mediated inflammation. To date, the potential effects of metformin on the gut mycobiome are entirely unknown. Therefore, this study aims to address this knowledge gap by characterizing the impact of metformin on the gut mycobiome of healthy adults and adults with pre‐diabetes and T2D, defined by fasting plasma glucose values. We searched for published research articles with archived, publicly accessible shotgun metagenomics data and re‐processed the data with one uniform bioinformatics pipeline to identify fungal taxa and relative abundance. Our analysis involved a total of 4510 samples from 13 individual studies ranging from randomized clinical trials to cross‐sectional cohorts. We performed analyses on the compiled dataset to (1) characterize the impact of metformin treatment in healthy, pre‐diabetic, and T2D individuals on the gut mycobiome; and (2) correlate the changes in relative abundance of fungal taxa to available clinical covariates, such as body mass index and fasting blood glucose. Secondary analysis of a randomized controlled trial of 44 newly diagnosed, treatment‐naïve T2D patients who were prescribed metformin for three days demonstrated a significant effect of metformin on the gut mycobiome richness (Shannon and Simpson indices; t test p = 0.02 and p = 0.0061 respectively) and diversity (PERMANOVA p = 0.001). Additionally, the relative abundance of Saccharomyces,a well‐characterized yeast genus, was significantly higher after three days of metformin treatment (Wilcoxon p = 0.019). This study provides novel insight into the interactions between human hosts, the gut microbiome, and the gut mycobiome in response to metformin, a widely used drug to treat T2D. Furthermore, these analyses may provide greater understanding of the role of the mycobiome‐microbiome interaction in metabolic diseases.

Chronic Exposure to Sublethal Concentrations of Aquatic Nitrite Change Nose and Gut Morphology and Associated Microbiomes in Channel Catfish

Nitrite is a common pollutant that can enter waterways via agricultural runoff or build up in aquaculture ponds when nitrogenous waste is converted to nitrite. Preliminary studies by the Huertas lab found that exposure to sublethal concentrations of aquatic nitrite alters the microbiome of goldfish and bioaccumulates in the olfactory epithelia, gills and brain. These studies also showed a negative impact on the olfactory tissue of exposed fish, which could lead to higher susceptibility to nasal pathogens. Our objective is to assess nitrite bioaccumulation in tissues and the alteration of the microbiome in the key aquaculture species channel catfish (Ictalurus punctatus). We hypothesize that the relative abundance and diversity of bacteria in the nose and gut microbiomes of channel catfish will be altered due to elevated nitrite exposure and that nitrite will bioaccumulate in tissues.Channel catfish were exposed to 0 mM (control), 0.2 mM, and 2 mM concentrations of nitrite. A total of six 500 liter tanks were used in a two‐phase experiment. For phase one, 16 fish per tank were placed into three 0 mM nitrite tanks and three 2 mM nitrite tanks. The 2 mM fish were kept for 12 hours before sampling. For phase two, 24 of the phase one control fish were placed into three 0.2 mM tanks and the remaining 24 control fish were left in the three control tanks for a total of 8 fish per tank. Phase two lasted 30 days with sub‐samplings at day five and 30. All fish were sampled for nose, gut, muscle, gill, brain, blood, liver, and kidney tissues for biochemical, microbial, or histological analysis. Upon dissection, fish from the 2 mM tanks exhibited marked methemoglobinemia due to nitrite‐induced oxidation of hemoglobin. The mortality rates were 0.04%, 0.08%, and 92% for the control, 0.2 mM, and 2 mM treatments respectively. The nose and gut microbiomes will be sequenced using whole genome shotgun sequencing to determine the microbial composition and measure changes in relative abundance. Histological analysis showed oxidative damage in all tissues from individuals exposed to 2 mM and partial damage in tissues of the 0.2 mM treatment.Because the microbiome is a powerful barrier against pathogens, disruption of the microbiome could lead to higher rates of disease infection and transmission in fish. Alteration of the nasal microbiome may increase mortality from the bacteria that cause septicemia in catfish, Edwardsiella ictaluri, whose common routes of infection are the nose or gut. Changes to the microbiome could be the missing link between nitrite and increased susceptibility to E. ictaluri infections in intensive farming. In the long term, this research aims to provide guidelines for water quality management in order to decrease the rate of bacterial infection and transmission in aquaculture systems.

Intestinal inflammation alters the antigen-specific immune response to a skin commensal.

SUMMARYResident microbes in skin and gut predominantly impact local immune cell function during homeostasis. However, colitis-associated neutrophilic skin disorders suggest possible breakdown of this compartmentalization with disease. Using a model wherein neonatal skin colonization by Staphylococcus epidermidis facilitates generation of commensal-specific tolerance and CD4+ regulatory T cells (Tregs), we ask whether this response is perturbed by gut inflammation. Chemically induced colitis is accompanied by intestinal expansion of S. epidermidis and reduces gut-draining lymph node (dLN) commensal-specific Tregs. It also results in reduced commensal-specific Tregs in skin and skin-dLNs and increased skin neutrophils. Increased CD4+ circulation between gut and skin dLN suggests that the altered cutaneous response is initiated in the colon, and resistance to colitis-induced effects in Cd4creIl1r1fl/fl mice implicate interleukin (IL)-1 in mediating the altered commensal-specific response. These findings provide mechanistic insight into observed connections between inflammatory skin and intestinal diseases.

Roadmap from Microbial Communities to Individuality Modeling for Anaerobic Digestion of Sewage Sludge.

Biological models describing anaerobic digestion (AD) of sewage sludge have been widely applied to test various control and operation strategies. Anaerobic digestion model 1 (ADM1) provides a generic platform that includes the main processes of AD, excluding homoacetogenesis and the microbial structure. Homoacetogenic bacteria have been identified as important competitors for hydrogen consumption and acetate production. Although recent advances in meta-omics techniques have improved our characterization of AD microbial communities, conventional models treat functional groups as homogeneous and overlook the physiology and behavior of microbial individuality, limiting insights into mechanisms governing process performance. A novel microbial individuality model (MIM) that integrates kinetics, energetics, and agent-based modeling to describe a microbiome's behavior as heterogenic populations, including homoacetogenesis, was developed. The MIM was validated with two datasets from previous studies through daily biogas production, methane content, compound concentrations, and microbial relative abundance changes. The MIM identified the emergence of Methanosaeta at low concentrations of acetate. Moreover, this simulation supports experimental studies confirming that the overlooked homoacetogenesis is an important hydrogen sink in AD. Validated MIMs are expected to provide insights into syntrophic and competitive interactions among microbiomes in AD systems while testing different operational parameters in a virtual environment. The MIM offers a methodological framework to other biological treatment systems and their microbial community dynamics.

Interannual shifts in sea surface temperature and chlorophyl drive the relative abundance and group size of common bottlenose dolphins Tursiops truncatus on the Southeast Gulf of California

Despite being one of the most common odontocetes off Sinaloa (Mexican Pacific coast), basic studies on the ecology of common bottlenose dolphins (Tursiops truncatus) are scarce in the region. This study aimed to describe changes in the relative abundance, group size, and behavior of this species during 2007 – 2012. We used boat-based surveys and satellite images of sea surface temperature (SST) and chlorophyll-a (Chl-a) to model changes in dolphin relative abundance (RA) over time, using correlations in time series analyses. Overall, mean RA was 3.6 dolphins h-1 (SD = 8.0), and significantly higher RA (6.4 –16.7 dolphins h-1) occurred in 2008, 2011, 2012, which was concurrent with hydrographic effects of La Niña oceanographic conditions, as well as during the upwelling season (February – April) (SST: 17.3 – 25.0 °C; Chl-a: 3.7 – 21.4 mg m-3). Conversely, significantly lower RA values (0.5 – 3.8 dolphins h-1) occurred in 2007 and 2010 that were likely associated with El Niño effects on the biological productivity of the area (Chl-a: 0.3 – 7.6 mg m-3). We found significant correlations between monthly Chl-a and SST average values with mean bottlenose dolphins RA, and lags (22 – 29 days) in the trophic response to variations of the hydrographic parameters. Significantly larger dolphin groups were recorded during La Niña years possibly because of the higher availability of their prey. This hypothesis is supported by higher feeding frequencies (35 – 73%) observed during the upwelling seasons, especially during La Niña conditions, whereas the most frequent behavior throughout all other years was traveling (28 – 69%). Our results show that RA and group size of bottlenose dolphins inhabiting the waters off Sinaloa, Mexico, are likely influenced by the changes in hydrographic parameters, especially during extreme climatic events.

The Impact of Local Estrogen on the Urogenital Microbiome in Genitourinary Syndrome of Menopause: A Randomized-Controlled Trial.

The postmenopausal urinary bladder microbiome is not well defined. The aims of this study were to characterize the effect of vaginal estrogen on the vaginal and urinary bladder microbiome in postmenopausal women and describe any clinical associations with the symptoms of genitourinary syndrome of menopause. This was a participant-masked, randomized controlled trial comparing the effect of a 12-week course of an estrogen-containing vaginal ring to a placebo vaginal ring. Standardized evaluations were performed at baseline and 12 weeks. Vaginal samples were obtained for pH, vaginal maturation index, and microbiome analysis. Concomitant catheterized urine samples were obtained for microbiome analysis. 16S ribosomal RNA gene sequencing was performed to characterize the resident microbial communities, with Lactobacillus relative abundance as the primary outcome variable. Genitourinary syndrome of menopause symptoms was measured using validated questionnaires (Pelvic Floor Distress Inventory-Short Form, Female Sexual Function Index, Vulvovaginal Symptoms Questionnaire). Of the 39 postmenopausal women randomized, baseline characteristics were similar between arms, with a mean age of 62 years and mean vaginal pH of 5.0. Using intention-to-treat analysis, there were no significant changes in vaginal or urinary Lactobacillus relative abundance. Two participants in each arm removed their ring prior to the end of the study. Eighty percent of participants experienced at least 1 bothersome genitourinary syndrome of menopause symptom. Vulvovaginal dryness and urinary frequency were most common at baseline, whereas painful intercourse and urinary urgency were most common at the final visit, none of which were statistically significant. Our study did not show a significant change in the bacterial composition of the vaginal or urinary bladder microbiome after either vaginal ring in this relatively asymptomatic postmenopausal population.

Sulfite preservatives effects on the mouth microbiome: Changes in viability, diversity and composition of microbiota.

Processed foods make up about 70 percent of the North American diet. Sulfites and other food preservatives are added to these foods largely to limit bacterial contamination. The mouth microbiota and its associated enzymes are the first to encounter food and therefore likely to be the most affected. Eight saliva samples from ten individuals were exposed to two sulfite preservatives, sodium sulfite and sodium bisulfite. One sample set was evaluated for bacteria composition utilizing 16s rRNA sequencing, and the number of viable cells in all sample sets was determined utilizing ATP assays at 10 and 40-minute exposure times. All untreated samples were analyzed for baseline lysozyme activity, and possible correlations between the number of viable cells and lysozyme activity. Sequencing indicated significant increases in alpha diversity with sodium bisulfite exposure and changes in relative abundance of 3 amplicon sequence variants (ASV). Sodium sulfite treated samples showed a significant decrease in the Firmicutes/Bacteroidetes ratio, a marginally significant change in alpha diversity, and a significant change in the relative abundance for Proteobacteria, Firmicutes, Bacteroidetes, and for 6 ASVs. Beta diversity didn't show separation between groups, however, all but one sample set was observed to be moving in the same direction under sodium sulfite treatment. ATP assays indicated a significant and consistent average decrease in activity ranging from 24-46% at both exposure times with both sulfites. Average initial rates of lysozyme activity between all individuals ranged from +/- 76% compared to individual variations of +/- 10-34%. No consistent, significant correlation was found between ATP and lysozyme activity in any sample sets. Sulfite preservatives, at concentrations regarded as safe by the FDA, alter the relative abundance and richness of the microbiota found in saliva, and decrease the number of viable cells, within 10 minutes of exposure.

Effect of Long-Term Agricultural Management on the Soil Microbiota Influenced by the Time of Soil Sampling

Application of agrochemicals and mechanization enabled increasing agricultural productivity yet caused various environmental and soil health-related problems. Agricultural practices affect soil microorganisms, which are the key players of many ecosystem processes. However, less is known about whether this effect differs between time points. Therefore, soil was sampled in winter (without crop) and in summer (in the presence of maize) from a long-term field experiment (LTE) in Bernburg (Germany) managed either under cultivator tillage (CT) or moldboard plow (MP) in combination with either intensive nitrogen (N)-fertilization and pesticides (Int) or extensive reduced N-fertilization without fungicides (Ext), respectively. High-throughput sequencing of 16S rRNA gene and fungal ITS2 amplicons showed that changes in the microbial community composition were correlated to differences in soil chemical properties caused by tillage practice. Microbial communities of soils sampled in winter differed only depending on the tillage practice while, in summer, also a strong effect of the fertilization intensity was observed. A small proportion of microbial taxa was shared between soils from the two sampling times, suggesting the existence of a stable core microbiota at the LTE. In general, taxa associated with organic matter decomposition (such as Actinobacteria, Bacteroidetes, Rhizopus, and Exophiala) had a higher relative abundance under CT. Among the taxa with significant changes in relative abundances due to different long-term agricultural practices were putative pathogenic (e.g., Gibellulopsis and Gibberella) and beneficial microbial genera (e.g., Chitinophagaceae, Ferruginibacter, and Minimedusa). In summary, this study suggests that the effects of long-term agricultural management practices on the soil microbiota are influenced by the soil sampling time, and this needs to be kept in mind in future studies for the interpretation of field data.

Relationships Between Diurnal Changes of Tongue Coating Microbiota and Intestinal Microbiota.

The oral cavity and the intestine are the main distribution locations of human digestive bacteria. Exploring the relationships between the tongue coating and gut microbiota, the influence of the diurnal variations of the tongue coating microbiota on the intestinal microbiota can provide a reference for the development of the disease diagnosis and monitoring, as well as the medication time. In this work, a total of 39 healthy college students were recruited. We collected their tongue coating microbiota which was collected before and after sleep and fecal microbiota. The diurnal variations of tongue coating microbiota are mainly manifested on the changes in diversity and relative abundance. There are commensal bacteria in the tongue coating and intestines, especially Prevotella which has the higher proportion in both sites. The relative abundance of Prevotella in the tongue coating before sleep has a positive correlation with intestinal Prevotella; the r is 0.322 (p < 0.05). Bacteroides in the intestine had the most bacteria associated with the tongue coating and had the highest correlation coefficient with Veillonella in the oral cavity, which was 0.468 (p < 0.01). These results suggest that the abundance of the same flora in the two sites may have a common change trend. The SourceTracker results show that the proportion of intestinal bacteria sourced from tongue coating is less than 1%. It indicates that oral flora is difficult to colonize in the intestine in healthy people. This will provide a reference for the study on the oral and intestinal microbiota in diseases.

Antibiotic resistance gene profile in aerobic granular reactor under antibiotic stress: Can eukaryotic microalgae act as inhibiting factor?

Antibiotic resistance gene (ARG) pollution is critical environmental problem, and horizontal gene transfer acts as a driving evolutionary force. In theory, due to the phylogenetic distance between eukaryotes and prokaryotes, eukaryotic microalgae can be a natural barrier that plays a negative role in ARG transfer among the symbiotic bacteria to decrease ARG abundance in sludge during wastewater treatment. However, this hypothesis is far from proven and needs to be tested experimentally, so this study investigated the influence of eukaryote microalgae (Scenedesmus) on the ARG profile of symbiotic bacteria based on aerobic granular reactor. The results indicated that Scenedesmus symbiosis could affect ARG diversity of bacteria, and the detected numbers of ARG in aerobic granular sludge (AG) group and algae-bacteria granular consortia (AAG) group were 45–53 and 44–47, respectively. In terms of relative abundance, after target microalgae symbiosis, the total abundance of ARGs significantly decreased from 1.17 × 10°, 2.69 × 10° and 1.36 × 10−1 to 6.53 × 10−1, 9.64 × 10−1 and 1.04 × 10−1 in the systems with the addition of streptomycin, azithromycin and vancomycin, respectively (P < 0.05), yet there was no significant difference between AG and AAG under the stress of ampicillin, sulfamethazine and tetracycline (P > 0.05). Redundancy analysis showed that the eukaryotic microalgae were significant factor explaining the change in ARG relative abundance (P < 0.05), which contributed 15.3% of ARG variation. Furthermore, the results show that, except for the tetracycline treatment system, the total relative abundances of MGEs in the AAG under the stress of the other five antibiotics were 3.54 × 10−2-7.13 × 10−1, which were all significantly lower than those in the AG (8.38 × 10−2-1.59 × 10°). There was a more significant positive correlation relationship between ARGs and mobile genetic elements (MGEs) than that between ARGs and dominated bacteria.