Changes In Relative Abundance Research Articles

Eight years of manure fertilization favor copiotrophic traits in paddy soil microbiomes

The application of organic matter to agricultural land is an efficient way to maintain soil eco-sustainability through the mediation of the soil-dwelling microbiome. Despite their important role in soil health, trait-based changes within cross-kingdom microbial communities following organic fertilization in soils are still poorly characterized. Here, shotgun metagenomic sequencing was used to examine microbial taxonomic and functional composition when subjected to a fertilization gradient, in which increasing amounts of cow manure have been continuously applied to paddy lands over 8 years. Organic fertilization did not have significant effects on the richness and diversity of soil microbial communities (bacteria, archaea, or fungi), nor the overall archaeal or fungal community compositions. However, bacterial communities were highly responsive to the fertilization gradient, and a unidirectional and progressive shift was observed. Notably, over 95% of bacterial taxa showing significant changes in relative abundances could be classified as copiotrophic taxa, such as those assigned to the Proteobacteria and Actinobacteria; in contrast, those in non-fertilized soils were mostly assigned to Acidobacteria, which is an oligotrophic group. Coupled with these changes, indices such as the decreased ratios of unclassified bacterial taxa to the total taxa with fertilization provided both direct and indirect lines of evidence for shifts towards a higher proportion of microbes with a copiotrophic lifestyle in fertilized soils compared with controls. Besides, the relative abundances of functional genes responsible for nutrient cycles (e.g., nitrate and sulfur reduction) as well as the degradation of complex organic compounds (e.g., lignin) were generally enriched with fertilization compared with the controls, implying a potential for preferentially enhanced nutrient biogeochemical processes with the higher proportion of copiotrophic microbes in fertilized soils. The present work helps to identify trait-based shifts in cross-kingdom soil microbial communities under organic fertilization, for the better evaluation of sustainable eco-agricultural management from a microbial community viewpoint.

Long-term changes in occurrence, relative abundance, and reproductive fitness of bat species in relation to arrival of White-nose Syndrome in West Virginia, USA.

White‐nose syndrome (WNS) is a disease caused by the fungus Pseudogymnoascus destructans which has resulted in the deaths of millions of bats across eastern North America. To date, hibernacula counts have been the predominant means of tracking the spread and impact of this disease on bat populations. However, an understanding of the impacts of WNS on demographic parameters outside the winter season is critical to conservation and recovery of bat populations impacted by this disease. We used long‐term monitoring data to examine WNS‐related impacts to summer populations in West Virginia, where WNS has been documented since 2009. Using capture data from 290 mist‐net sites surveyed from 2003 to 2019 on the Monongahela National Forest, we estimated temporal patterns in presence and relative abundance for each bat species. For species that exhibited a population‐level response to WNS, we investigated post‐WNS changes in adult female reproductive state and body mass. Myotis lucifugus (little brown bat), M. septentrionalis (northern long‐eared bat), and Perimyotis subflavus (tri‐colored bat) all showed significant decreases in presence and relative abundance during and following the introduction of WNS, while Eptesicus fuscus (big brown bat) and Lasiurus borealis (eastern red bat) responded positively during the WNS invasion. Probability of being reproductively active was not significantly different for any species, though a shift to earlier reproduction was estimated for E. fuscus and M. septentrionalis. For some species, body mass appeared to be influenced by the WNS invasion, but the response differed by species and reproductive state. Results suggest that continued long‐term monitoring studies, additional research into impacts of this disease on the fitness of WNS survivors, and a focus on providing optimal nonwintering habitat may be valuable strategies for assessing and promoting recovery of WNS‐affected bat populations.

The Interplay of Phototrophic and Heterotrophic Microbes Under Oil Exposure: A Microcosm Study.

Microbial interactions influence nearly one-half of the global biogeochemical flux of major elements of the marine ecosystem. Despite their ecological importance, microbial interactions remain poorly understood and even less is known regarding the effects of anthropogenic perturbations on these microbial interactions. The Deepwater Horizon oil spill exposed the Gulf of Mexico to ∼4.9 million barrels of crude oil over 87 days. We determined the effects of oil exposure on microbial interactions using short- and long-term microcosm experiments with and without Macondo surrogate oil. Microbial activity determined using radiotracers revealed that oil exposure negatively affected substrate uptake by prokaryotes within 8 h and by eukaryotes over 72 h. Eukaryotic uptake of heterotrophic exopolymeric substances (EPS) was more severely affected than prokaryotic uptake of phototrophic EPS. In addition, our long-term exposure study showed severe effects on photosynthetic activity. Lastly, changes in microbial relative abundances and fewer co-occurrences among microbial species were mostly driven by photosynthetic activity, treatment (control vs. oil), and prokaryotic heterotrophic metabolism. Overall, oil exposure affected microbial co-occurrence and/or interactions possibly by direct reduction in abundance of one of the interacting community members and/or indirect by reduction in metabolism (substrate uptake or photosynthesis) of interacting members.

New Radiocarbon Constraints on the Global Cycling of Solid‐Phase Extractable Dissolved Organic Carbon

AbstractRadiocarbon (∆14C) measurements suggest the deep ocean stores marine dissolved organic carbon (DOC) on millennial timescales. The mechanisms that mediate this residence time remain unconstrained. Solid‐phase extraction (SPE) has emerged as a widely used technique to isolate DOC for subsequent analyses. We present SPE‐DOC concentrations and ∆14C values for three GO‐SHIP Repeat Hydrography transects, spanning the Pacific, Southern and Indian Oceans. Comparisons of SPE‐DOC with total DOC ∆14C values are used with an isotopic mass‐balance to estimate the size of the refractory DOC (RDOC) reservoir and changes in RDOC relative abundance in the global ocean. Estimated RDOC abundance is similar across the deep Pacific and Indian Oceans (average = 93 ± 5%, 35 ± 6 μM), whereas RDOC in the surface ocean varies as a function of total DOC concentration. Our results fill in spatial SPE‐DOC ∆14C sampling gaps for the global ocean, and our mass‐balance RDOC estimates are consistent with previous observations.

The Role of the Oral Microbiota in the Etiopathogenesis of Oral Squamous Cell Carcinoma.

Dysbiosis in the oral environment may play a role in the etiopathogenesis of oral squamous cell carcinoma (OSCC). This review aims to summarize the current knowledge about the association of oral microbiota with OSCC and to describe possible etiopathogenetic mechanisms involved in processes of OSCC development and progression. Association studies included in this review were designed as case–control/case studies, analyzing the bacteriome, mycobiome, and virome from saliva, oral rinses, oral mucosal swabs, or oral mucosal tissue samples (deep and superficial) and comparing the results in healthy individuals to those with OSCC and/or with premalignant lesions. Changes in relative abundances of specific bacteria (e.g., Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus sp.) and fungi (especially Candida sp.) were associated with OSCC. Viruses can also play a role; while the results of studies investigating the role of human papillomavirus in OSCC development are controversial, Epstein–Barr virus was positively correlated with OSCC. The oral microbiota has been linked to tumorigenesis through a variety of mechanisms, including the stimulation of cell proliferation, tumor invasiveness, angiogenesis, inhibition of cell apoptosis, induction of chronic inflammation, or production of oncometabolites. We also advocate for the necessity of performing a complex analysis of the microbiome in further studies and of standardizing the sampling procedures by establishing guidelines to support future meta-analyses.

The mudstone composition as reflected in the sedimentary evolution of a turbidite basin: The example of the Agnone Flysch (Molise, Italy)

Chemical and mineralogical signatures of mudstones from the Agnone Flysch turbidite successions (late Tortonian to early Messinian) deposited in the Lagonegro-Molise foredeep basin reveal new insight for the sedimentary evolution of the southern Apennines during late Miocene. Geochemical and mineralogical signatures of the Verrino and Poggio Villanelle members of the Agnone Flysch mark a complex sedimentation history testifying to a multi-source area probably due to structural changes and depositional basin physiography. The studied mudstones show chemical variations in term of Ca vs. Si and Al. Mineralogical analyses confirm a decrease of carbonate minerals and an increase of silicate phases passing from Verrino Member to Poggio Villanelle Member samples. Compositional data of the mudstone samples of both members mainly record a derivation from felsic rocks due to the Calabrian terranes unroofing. Poggio Villanelle Member samples further show an enrichment in Cr, Ni, Fe e Mg in accordance with higher chlorite content suggesting a mafic supply probably related to an ophiolitic source successively exposed. Thus, those trends based on chemical and mineralogical data suggest a change in relative abundance of a detritus characterized by different compositions through time and space. Whole rock geochemistry of the studied mudstones indicate that they are from the first-cycle sediments.Palaeoweathering processes in source areas were moderate as shown by CIA (Chemical Index of Alteration) and CIA’ (modified Chemical Index of Alteration) values of the mudstones of both members (Verrino and Poggio Villanelle members). The trends observed in the paleoweathering diagrams suggest source areas characterized by moderate weathering in non-steady-state conditions which have changed toward the upper portion of the sedimentary succession. Those changes are mainly related to the geodynamic conditions of the source areas where active tectonism allows erosion of all zones within weathering profiles developed on source rocks.The paleocurrent data and the compositional analysis of the mudstones and sandstones indicate a provenance (supply) from the western, north-western, and south-western sectors of the basin where carbonate platforms and magmatic, metamorphic and sedimentary rocks cropped out.

High Counts and Anthracene Degradation Ability of Streptococcus mutans and Veillonella parvula Isolated From the Oral Cavity of Cigarette Smokers and Non-smokers.

The composition and metabolic functions of oral microbiota are affected by many factors including smoking leading to several health problems. Cigarette smoking is associated with changes in oral microbiota composition and function. However, it is not known if the depletion of certain bacterial genera and species is due to specific toxins in cigarette smoke, or indirectly due to competition for colonization with smoking-enriched bacteria. Therefore, the aim of this study was to determine the effect of cigarette smoking on the microbial prevalence and polycyclic aromatic hydrocarbons (PAHs) biodegradation of selected enriched and depleted oral bacteria from oral microbiota of smokers compared to that in non-smokers. Samples of oral rinse from smokers and non-smokers were collected (n = 23, 12 smokers and 11 non-smokers) and screened for oral bacterial strains of Streptococcus mutans, Lactobacillus spp., and Veillonella spp. Comparing counts, S. mutans, V. tobetsuensis, and V. dispar showed higher counts in smokers compared to non-smokers while the Lactobacillus spp. were higher in non-smokers. Lactobacillus fermentum was prevalent in smokers, representing 91.67% of the total Lactobacillus spp. isolates. The biodegradation potential of anthracene; a representative of PAHs of collected isolates, in single and mixed cultures, was assayed with anthracene as the sole source of carbon using 2,6-dichlorophenol indophenol (2,6-DCPIP) as indicator. S. mutans isolates recovered from smokers showed higher degradation of anthracene compared to those recovered from non-smokers. The anaerobic anthracene biodegradation activity of V. parvula isolates from non-smokers was the highest among all isolates of the three recovered genera from the same subject. The anthracene biodegradation potential of Lactobacillus spp. was variable. Combinations of isolated bacteria in co-cultures showed that Lactobacillus spp. interfered with anthracene biodegradation ability along with the viable counts of S. mutans and Veillonella spp. In conclusion, oral dysbiosis due to cigarette smoking was observed not only due to changes in oral bacterial relative abundance but also extended to bacterial functions such as anthracene biodegradation tested in this study. Microbe–microbe interactions changed the anthracene biodegradation potential and growth of the microbial mixture compared to their corresponding single isolates, and these changes differ according to the constituting bacteria.

Role of Bacillus inoculation in rice straw composting and bacterial community stability after inoculation: Unite resistance or individual collapse

Bacillus is the classic inoculant in rice straw composting. However, there has been no in-depth study of the mechanism promoting the degradation of lignocellulose and the change of indigenous bacterial communities after Bacillus inoculation. Moreover, the stability of bacterial communities is a significant challenge in achieving the efficacy of inoculation. In this study, the ecological succession and yield-resource acquisition-stress tolerance (Y-A-S) framework were combined with Redundancy analysis (RDA) and changes in relative abundance, Bacillus was found to be a pioneer bacterium that adopts a resource acquisition-stress tolerance strategy. The structural equation model (SEM) revealed that in addition to exerting a degradation effect, Bacillus inoculation could also indirectly affect lignocellulose degradation by changing the bacterial community. Random forest model and network analysis indicated a change in bacterial communities after inoculation, and bacteria with more complex relationships and weaker decomposition ability were key to the stability of bacterial communities.

Spatiotemporal dynamics of insect pollinator communities in sagebrush steppe associated with weather and vegetation

The conservation of native insect pollinators is hampered by a lack of information about environmental factors influencing pollinator communities. We investigated how insect pollinator communities, composed of bees (Hymenoptera), butterflies and moths (Lepidoptera), and flies (Diptera), are influenced by spatial and temporal aspects of the environment in sagebrush steppe shrublands. We assessed hypotheses regarding spatial autocorrelation of communities, inter-annual variability in communities, influence of elevation on timing of emergence, and influence of weather on seasonal changes in relative abundance of different pollinator taxa. We captured 27,310 insects from 6 bee families, 27 butterfly and moth families, and 3 fly families. The occurrence of insect pollinators among sampling plots was not spatially autocorrelated, indicating that insect communities may be structured by habitat variation and microclimates over relatively fine spatial scales. Pollinator familial richness, diversity, abundance, and timing of emergence were most strongly positively associated with spatiotemporal variation in minimum daily temperatures at the ground surface during the active season. Emergence timing was positively correlated with growing degree days and percent humidity, regardless of elevation. All pollinator groups varied in abundance throughout their active season, peaking in early July (bees), late July (flies), or early August (butterflies and moths). Our findings suggest that changes in nighttime temperatures, which have been steadily increasing over the last several decades as a result of climate change, may have strong effects on sagebrush steppe pollinator communities. Also, non-bee pollinators may provide particularly important pollination in this vast ecosystem during the warmest time of the year.

Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.

Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic-pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water-sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton-derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water-sediment interface showed that bacterial α-diversity was not affected by POM addition, while bacterial β-diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom- or cyanobacteria-favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton-originated POM can impact bacterial dynamics at the water-sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic-pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.

Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca

We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.

506-P: Weight Loss Is Associated with Changes in Gut Microbiome: A Randomized, Crossover Trial Comparing a Mediterranean and a Low-Fat Vegan Diet in Overweight Adults

Background: Mediterranean and vegan diets improve body weight and gut microbiome composition. The aim of this study was to compare both diets head-to-head. Methods: Randomized cross-over trial, conducted February-October 2019. Sixty-two overweight adults were assigned to each diet for 16-week periods in random order, separated by a 4-week washout. Body weight was the primary outcome. Secondary measures included changes in gut microbiome which was measured using 16S rRNA sequencing. Results: Body weight decreased on the vegan compared with the Mediterranean diet (treatment effect -6.0 kg [95% CI -7.5 to -4.5]; p<0.001). The relative abundance of Bacteriodetes decreased (p<0.001 for both diets) and Eubacteria increased on both diets (p<0.001 for the Mediterranean and p=0.009 for the vegan diet). The relative abundance of Lachnospiraceae increased (p=0.03), the Firmicutes to Bacteroidetes ratio increased (p=0.04) and the butyrate-producing bacteria decreased (p=0.02) on the Mediterranean diet. The relative abundance of Proteobacteria decreased (p<0.001), and Enterobacteria and Ruminococcus increased on the vegan diet (p=0.04 and p<0.001, respectively). Changes in body weight correlated positively with changes in relative abundance of Firmicutes both on the Mediterranean (r=+0.36; p=0.01) and the vegan diet (r=+0.41; p<0.001) and with changes in relative abundance of Lachnospiraceae both on the Mediterranean (r=+0.40; p<0.001) and the vegan diet (r=+0.44; p<0.001). In addition, the changes in body weight correlated negatively with changes in relative abundance of Enterobacteria on the Mediterranean diet (r=-0.32; p=0.02) and Eubacteria on the vegan diet (r=-0.49; p<0.001). Conclusions: A low-fat vegan diet lead to a greater weight loss compared with a Mediterranean diet. This may be partly explained by the difference in gut microbiome composition. Disclosure H. Kahleova: None. R. Holubkov: Advisory Panel; Self; National Institutes of Health, U. S. Food and Drug Administration, Board Member; Self; Pfizer Inc., Revance Therapeutics. N. Barnard: None. Funding Physicians Committee for Responsible Medicine

Zebrafish Chromosome 14 Gene Differential Expression in the fmr1 h u2787 Model of Fragile X Syndrome.

Zebrafish represent a valuable model for investigating the molecular and cellular basis of Fragile X syndrome (FXS). Reduced expression of the zebrafish FMR1 orthologous gene, fmr1, causes developmental and behavioural phenotypes related to FXS. Zebrafish homozygous for the hu2787 non-sense mutation allele of fmr1 are widely used to model FXS, although FXS-relevant phenotypes seen from morpholino antisense oligonucleotide (morpholino) suppression of fmr1 transcript translation were not observed when hu2787 was first described. The subsequent discovery of transcriptional adaptation (a form of genetic compensation), whereby mutations causing non-sense-mediated decay of transcripts can drive compensatory upregulation of homologous transcripts independent of protein feedback loops, suggested an explanation for the differences reported. We examined the whole-embryo transcriptome effects of homozygosity for fmr1hu2787 at 2 days post fertilisation. We observed statistically significant changes in expression of a number of gene transcripts, but none from genes showing sequence homology to fmr1. Enrichment testing of differentially expressed genes implied effects on lysosome function and glycosphingolipid biosynthesis. The majority of the differentially expressed genes are located, like fmr1, on Chromosome 14. Quantitative PCR tests did not support that this was artefactual due to changes in relative chromosome abundance. Enrichment testing of the “leading edge” differentially expressed genes from Chromosome 14 revealed that their co-location on this chromosome may be associated with roles in brain development and function. The differential expression of functionally related genes due to mutation of fmr1, and located on the same chromosome as fmr1, is consistent with R.A. Fisher’s assertion that the selective advantage of co-segregation of particular combinations of alleles of genes will favour, during evolution, chromosomal rearrangements that place them in linkage disequilibrium on the same chromosome. However, we cannot exclude that the apparent differential expression of genes on Chromosome 14 genes was, (if only in part), caused by differences between the expression of alleles of genes unrelated to the effects of the fmr1hu2787 mutation and made manifest due to the limited, but non-zero, allelic diversity between the genotypes compared.

Biodegradation of foam plastics by Zophobas atratus larvae (Coleoptera: Tenebrionidae) associated with changes of gut digestive enzymes activities and microbiome

In order to uncover the plastic types that superworm Zophobas atratus can degrade and the underlying changes associated with plastics consumption, three types of plastics including polystyrene (PS), polyethylene (PE) and polyurethane (PU) foam were used as sole feedstock to feed the superworm larvae for 35 days with bran as control. Compared to the control, PS- or PU-fed larvae showed 100% survival rates, the PE-fed and starvation larvae had decreased survival rates of 81.67% and 65%, respectively. Both plastics-fed and starvation groups showed decreased larvae weight. The consumption rates of PS, PE, and PU were 1.41, 0.30, and 0.74 mg/d/larva, respectively. The attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and differential scanning calorimeter and thermogravimetric (DSC-TGA) analyses demonstrated the changes of functional groups and thermostability in frass compared to plastic feedstocks, indicating the partial oxidation and degradation of plastics. Among the gut digestive enzymes tested, protease showed increased activities in all plastics-fed groups. Gut microbial communities displayed significant relative abundance changes such as increased abundances of Enterococcus in all plastic-fed groups, Citrobacter in PE-fed group, Dysgonomonas and Sphingobacterium in PS-fed group, and Mangrovibacter in PU-fed group. The latter 3 genera were reported for the first time. In summary, the results demonstrated that Z. atratus could efficiently degrade both PS and PU foam plastics, and the plastic degradation was associated with changes of gut microbial communities and digestive enzyme activities.

Functional biogeography of Neotropical moist forests: Trait–climate relationships and assembly patterns of tree communities

AbstractAimHere we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait–climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator, but also in terms of abundance in local communities in currently wetter, warmer and more seasonal climates.LocationNeotropics.Time periodRecent.Major taxa studiedTrees.MethodsWe obtained abundance data from 471 plots across nine Neotropical regions, including c. 100,000 trees of 3,417 species, in addition to six functional traits. We compared occurrence‐based trait distributions among regional species pools, and evaluated single trait–climate relationships across local communities using community abundance‐weighted means (CWMs). Multivariate trait–climate relationships were assessed by a double‐constrained correspondence analysis that tests both how CWMs relate to climate and how species distributions, parameterized by niche centroids in climate space, relate to their traits.ResultsRegional species pools were undistinguished in functional terms, but opportunistic strategies dominated local communities further from the equator, particularly in the Northern Hemisphere. Climate explained up to 57% of the variation in CWM traits, with increasing prevalence of lower‐statured, light‐wooded and softer‐leaved species bearing smaller seeds in more seasonal, wetter and warmer climates. Species distributions were significantly but weakly related to functional traits.Main conclusionsNeotropical moist forest regions share similar sets of functional strategies, from which local assembly processes, driven by current climatic conditions, select for species with different functional strategies. We can thus expect functional responses to climate change driven by changes in relative abundances of species already present regionally. Particularly, equatorial forests holding the most conservative traits and large seeds are likely to experience the most severe changes if climate change triggers the proliferation of opportunistic tree species.

The effect of local estrogen therapy on the urinary microbiome composition of postmenopausal women with and without recurrent urinary tract infections.

Recurrent urinary tract infections (rUTIs) occur in 2-10% of postmenopausal women. Local estrogen therapy (LET) has been shown to reduce UTIs. This study aimed to compare the urinary microbiome between patients with and without a history of rUTIs and to examine whether treatment with LET influences the diversity and richness of microbiome species in two groups. Postmenopausal women with and without rUTIs attending the urogynecology clinic between April 2019 and December 2020 were recruited. Participant baseline characteristics and demographics were recorded. Aseptic transurethral urine samples were collected at recruitment and at 3-6months following treatment with LET. The V1-V2 and ITS regions of the 16S rRNA gene were sequenced to identify bacteria. A total of 37 women were recruited, 20 controls and 17 patients with rUTI. During follow-up, symptomatic UTIs occurred in 3/17 (17.6%) and 0/20 in the rUTI group and control group, respectively. Klebsiella aerogenes was present in 80% of rUTI samples and in 53.3% of control samples before LET. Abundance of Finegoldia magna was present in 33.3% of samples before LET, but only in 6.7% after LET. There was no change in relative abundance of lactobacillus species following LET in both groups. Treatment with vaginal LET altered the local hormonal environment of the urinary bladder and likely protected women from development of rUTI by decreasing the presence of F. magna. To confirm the significance of this bacterial species in rUTI symptomatology, our finding needs to be validated on a larger patient cohort.

Abnormalities in the composition of the gut microbiota in mice after repeated administration of DREADD ligands

Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) are known as genetically modified G-protein-coupled receptors (GPCRs), which can be activated by synthetic ligands such as clozapine N-oxide (CNO) and DREADD agonist 21 (compound 21: C21). The brain-gut-microbiota axis has a crucial role in bidirectional interactions between the brain and the gastrointestinal microbiota. In this study, we investigated whether repeated administration of CNO or C21 could influence the gut microbiota and short-chain fatty acids (SCFAs) in feces of adult mice. Repeated administration of CNO or C21 as drinking water did not alter the α- and β-diversity of gut microbiota in mice compared with control mice. However, we found significant changes in relative abundance for several bacteria in the CNO (or C21) group at the taxonomic level compared to the control group. The linear discriminant analysis effect size (LEfSe) algorithm distinguished the family Prevotellaceae, the genus Anaerocolumna, the genus Prevotella, and the genus Frisingicoccus, these four specific microbial markers for the CNO group relative to the control group. In addition, the LEfSe algorithm identified the family Clostridiaceae, the genus Faecalicatena and the genus Marinisporobacter, these three bacteria of different taxonomic as potential microbial markers for the C21 group relative to the control group. In contrast, repeated administration of CNO (or C21) did not alter SCFAs in feces samples of adult mice. The data suggest that repeated administration of CNO or C21 contributes to an unusual organization of the gut microbiota in adult mice. Therefore, abnormalities in the composition of gut microbiota by repeated dosing of DREADD ligands should be taken into consideration for behavioral and biological functions in rodents treated with DREADD ligands.

Effects of chloramphenicol on the bacterial community structure and simultaneous nitrification and denitrification performance in a sequencing biofilm batch reactor

The effects of chloramphenicol (CAP) on the performance of simultaneous nitrification and denitrification (SND), as well as on the bacterial community, were evaluated in a sequencing biofilm batch reactor (SBBR). The chemical oxygen demand (COD) removal decreased as the CAP concentration increased from 0 to 20 mg/l. But CAP had different effects on nitrification and denitrification: in contrast to continuously inhibiting nitrification, 15 mg/l CAP slightly promoted denitrification. Besides, the specific oxygen utilization rate declined with increasing CAP concentration, and the nitrifying and denitrifying rates initially displayed a trend of decreasing, and then increasing and finally decreasing, with increases in CAP concentration. In addition, the SBBR process exhibited an excellent ability to degrade CAP, especially when its concentration was 20 mg/l. The high-throughput sequencing results indicated that some obvious variations in the bacterial community at different CAP concentrations—in particular relative abundance changes in the dominant bacterial species at the phylum, class and genus levels. Overall, this study reveals that the effects of CAP on the nitrogen (N) removal performance in SBBR, provides a theoretical guide for SBBR treatment of practical wastewater.

Structure and composition of barley rhizospheric bacterial community and plant development cultivated with a super absorbent polymer

ABSTRACT Our study aimed to determine the effect on barley (Hordeum vulgare L.) of adding potassium polyacrylate to a sandy soil under normal watering condition and drought. We focused on morphological and physiological characteristics of barley and its rhizosphere bacterial community structure using Illumina Miseq sequencing. It was found that under normal watering condition (70% of soil water holding capacity (WHC)), the soil water retention increased with the SAP addition to the soil. Barley plant height and weight, leaf relative water content and protein content decreased under drought (35% of soil WHC), the addition of SAP eliminated the negative effect of drought on plants, the proline content was reduced from 2.71 μg g−1 leave dry weight with stressed plants to 0.99 μg g−1 with only 0.2% of SAP. The barley rhizophere bacterial community was affected by drought. Changes in relative abundance were noticed at both phyla and OTU level. The SAP addition (0.8%) shifted the barley rhizophere bacterial community to become in part more similar to that of the normal watering condition. Also, we found that the SAP addition had a side effect itself on the barley rhizosphere bacterial community other than its capacity of water holding.

Capturing aerial insects available as food for chimney swifts in western Pennsylvania using a tethered balloon

Abstract This study presents the relative abundance of aerial insects available for chimney swifts (Chaetura pelagica) to eat in Indiana, Pennsylvania in April, May, and June of 2006. Aerial insects were captured on acrylic “sticky traps” attached to the tether rope of a 3.048-m-diameter helium balloon at heights of 27 to 55 m above the ground. The methodology is evaluated, and we conclude that the described method can be carried out successfully and does provide useful data, but also has practical difficulties. The total sample size was 716 individual organisms (685 insects and 31 spiders) captured over 115.84 collecting hours. This study provides baseline information and recommendations for future studies within the context of conservation, especially concerning changes in relative abundance of aerial insect orders used for food by insectivores, such as chimney swifts. Historical and current aerial insect sampling methods are discussed.