Greater Relative Abundance Research Articles

Effects of Dietary Supplementation with High Fiber (Stevia Residue) on the Fecal Flora of Pregnant Sows.

Simple SummaryThis study aimed to investigate the effects of different supplementation levels of stevia residues in high-fiber diets on the fecal microorganisms of pregnant sows. Stevia residue supplementation significantly increased the abundance of beneficial bacteria, such as g__Lachnospiraceae_XPB1014_group, g__Christensenellaceae_R-7_group, and g__Ruminococcaceae_UCG-005 (p < 0.05), and significantly reduced the abundance of harmful bacteria, such as Treponema_2 (p < 0.05), at the genus level. The stevia-residue supplementation reduced the feed cost, with the highest reduction rate being 13.33%. In conclusion, high-fiber diets can improve the intestinal balance and evenness index of the intestinal flora in pregnant sows, promote the relative abundance of beneficial bacteria, reduce the relative abundance of harmful bacteria, and reduce feed cost.This study aimed to investigate the effects of different supplementation levels of stevia residues in high-fiber diets on the fecal microorganisms of pregnant sows. Forty-eight first-farrowing Danish Landrace sows with similar weight, age, and due date were randomly divided into four groups. The control group was fed a normal diet (CON; 3.15% crude fiber content), and the treatment groups were supplemented with 20% stevia residue (SRL), 30% stevia residue (SRM), or 40% stevia residue (SRH) stevia residue, with crude fiber content of 7.79%, 9.15%, and 10.68%, respectively. The test period was 135 days, and Illumina Miseq high-throughput sequencing was used to test the fecal bacteria of the pregnant sows on day 56. Compared to the control group, species diversity was greater in the 30% stevia residue group. At the phylum level, Firmicutes and Spirochaetes had the greatest relative abundances; Firmicutes was most abundant in the SRM group, and Spirochaetes was most abundant in the CON group. At the genus level, Lactobacillus, Streptococcus, and Lachnospiraceae_XPB1014_group, and Treponema_2 had the highest relative abundances in the stevia-residue treatments. Among them, Lactobacillus and Treponema_2 were more abundant in SRL, Streptococcus was more abundant in SRH, and Lachnospiraceae_XPB1014_group was more abundant in SRM. Linear discriminant analysis effect size (LEfSe) showed that the bacterial species differed among the stevia residue treatments. SRL mainly included g__Lactobacillus and g__Romboutsi, SRM mainly included g__Lachnospiraceae_XPB1014_group and g__Ruminococcaceae_UCG_014, SRH mainly included g__Streptococcus, and CON mainly included g__Treponema_2, f__Clostridiaceae_1, g__norank_f__Muribaculaceae, and g__norank_f__p_251_o5. Stevia-residue supplementation significantly increased the abundance of beneficial bacteria, such as g__Lachnospiraceae_XPB1014_group, g__Christensenellaceae_R-7_group, and g__Ruminococcaceae_UCG-005 (p < 0.05), and significantly reduced the abundance of harmful bacteria, such as Treponema_2 (p < 0.05). Moreover, compared with the control group, the stevia-residues treatment groups reduced the feed cost 8.33%, 12.50%, and 13.33% per sow per day, respectively. In conclusion, high-fiber diets can improve the intestinal balance and evenness index of the intestinal flora in pregnant sows, promote the relative abundance of beneficial bacteria, reduce the relative abundance of harmful bacteria, and reduce feed cost. The optimal supplementation level of the stevia residue was found to be 30%.

246 Effect of increasing levels of dietary starch on equine cecal microbiota

Abstract An experiment was conducted with 6 cecally cannulated horses (524 ± 65.5 kg BW) to evaluate effects of increasing dietary starch on equine cecal microbiota. Starch was supplied via corn pellets and was increased by 0.5 g starch/kg BW/meal every 7 d until horses received 3.5 g starch/kg BW/meal. Throughout the experiment, Smooth Bromegrass hay and water were offered ad libitum. Meals were fed every 6 h, starting at 0600 h. On d 7 of each period, cecal digesta was collected every 2 h for 12 h. Within period, cecal samples for each horse were pooled and DNA was extracted for PCR amplification of the 16 S rRNA gene (V3 and V4 regions) and sequencing via Illumina MiSeq. Alpha and beta diversity were measured. Data were analyzed as a randomized complete block with fixed effect of starch level and random effect of horse (SAS version 9.4). If a horse presented with colic, it was removed from the experiment. Parameters when feeding 1.5 g starch/kg BW/meal were compared between horses which completed the trial and those removed using covariate of 0 g starch/kg BW/meal. Feeding 1.5 g starch/kg BW/meal elicited the greatest changes in microbiota, indicated by reduced (P ≤ 0.02) operational taxonomical units and Faith phylogenetic diversity and different (P ≤ 0.017) beta diversity compared to all other treatments. Across treatments, Firmicutes was the most abundant phyla, followed by Bacteroidetes. Feeding 1.5 g starch/kg BW/meal led to lowest (P ≤ 0.0342) relative abundance (RA) of Prevotella, Treponema, Phascolarctobacterium, and [Prevotella]. Horses that persisted throughout the experiment had reduced (P = 0.0163) RA of Ruminococcus and greater RA of Phascolarctobacterium (P = 0.0057) when consuming 1.5 g starch/kg BW/meal compared to those removed. This is the first report describing effects of gradually increasing dietary starch on equine cecal microbiota in vivo.

Bacterial Communities of Ballan Wrasse (Labrus bergylta) Eggs at a Commercial Marine Hatchery

Ballan wrasse (Labrus bergylta, Ascanius 1767) are cleaner fish cultured in northern Europe to remove sea lice from farmed Atlantic salmon (Salmo salar, Linnaeus 1758). Despite increasing appreciation for the importance of the microbiota on the phenotypes of vertebrates including teleosts, the microbiota of wrasse eggs has yet to be described. Therefore, the aim of this present study was to describe the bacterial component of the microbiota of ballan wrasse eggs shortly after spawning and at 5 days, once the eggs had undergone a routine incubation protocol that included surface disinfection steps in a common holding tank. Triplicate egg samples were collected from each of three spawning tanks and analysis of 16S rRNA gene sequences revealed that 88.6% of reads could be identified to 186 taxonomic families. At Day 0, reads corresponding to members of the Vibrionaceae, Colwelliaceae and Rubritaleaceae families were detected at greatest relative abundances. Bacterial communities of eggs varied more greatly between tanks than between samples deriving from the same tank. At Day 5, there was a consistent reduction in 16S rRNA gene sequence richness across the tanks. Even though the eggs from the different tanks were incubated in a common holding tank, the bacterial communities of the eggs from the different tanks had diverged to become increasingly dissimilar. This suggests that the disinfection and incubation exerted differential effects of the microbiota of the eggs from each tank and that the influence of the tank water on the composition of the egg microbiota was lower than expected. This first comprehensive description of the ballan wrasse egg bacterial community is an initial step to understand the role and function of the microbiota on the phenotype of this fish. In future, mass DNA sequencing methods may be applied in hatcheries to screen for pathogens and as a tool to assess the health status of eggs.

Remediation of selenium-contaminated soil through combined use of earthworm Eisenia fetida and organic materials

Selenium (Se)-polluted soils pose serious threats to terrestrial ecosystems through food chains. This study evaluated the use of earthworm Eisenia fetida and organic materials for Se remediation. The greater mortality (6.7%) and weight loss (28.6%) were observed for earthworms exposed to selenate than selenite at 20 mg Se Kg−1 over 21 d, while selenate was taken up 2.5-fold faster than selenite. Compared with peat moss, Se accumulation increased by 119% in selenite-exposed earthworms supplied with cow manure. Earthworm activity caused greater reduction in selenite (17.4%), with little impact on selenate-treated soil. X-ray absorption spectroscopy speciation analysis shows 87–91% of tissue Se was transformed to organo-Se, i.e., SeMet and SeCys, in earthworms exposed to either selenite or selenate, posing great risks to their predators. The study also found selenium increased bacterial diversity in earthworm casts, while greater relative abundances (~37.57%) of functional genera were obtained for selenite. Over 24 h, two bacteria strains, Bacillus cereus and Aeromonas encheleia, isolated from casts, rapidly reduced selenite by ~94%, compared to ~25% for selenate. Elemental Se was present only in strains (~27%), casts (~11%) and worm-inhabited soil (~2.7%) of selenite treatments, suggesting earthworm gut microbiota could buffer earthworms and other soil fauna from selenite toxicity.

Characterization of the Bacterial Biofilm Communities Present in Reverse-Osmosis Water Systems for Haemodialysis.

Biofilm in reverse osmosis (RO) membranes is a common problem in water treatment at haemodialysis facilities. Bacteria adhere and proliferate on RO membranes, forming biofilms, obstructing and damaging the membranes and allowing the transfer of bacteria and/or cellular components potentially harmful to the health of haemodialysis patients. Our aim was to characterize the bacterial community associated to biofilm of RO membranes and to identify potentially pathogenic bacteria present in the haemodialysis systems of two dialysis centres in Chile. The diversity of the bacterial communities present on RO membranes and potable and osmosed water samples was evaluated using Illumina sequencing. Additionally, bacteria from potable water, osmosed water and RO membrane samples were isolated, characterized and identified by Sanger’s sequencing. The molecular analyses of metagenomics showed that the phyla having a greater relative abundance in both dialysis centres were Proteobacteria and Planctomycetes. Pseudomonas, Stenotrophomonas, Agrobacterium, Pigmentiphaga, Ralstonia, Arthrobacter, Bacteroides and Staphylococcus were bacterial genera isolated from the different samples obtained at both haemodialysis centres. Pseudomonas spp. was a bacterial genus with greater frequency in all samples. Pseudomonas and Staphylococcus showed higher levels of resistance to the antibiotics tested. Results demonstrated the presence of potentially pathogenic bacteria, showing resistance to antimicrobials on RO membranes and in osmosed water in both dialysis centres studied.

Dependence of the Staphylococcal Volatilome Composition on Microbial Nutrition.

In vitro cultivation of staphylococci is fundamental to both clinical and research microbiology, but few studies, to-date, have investigated how the differences in rich media can influence the volatilome of cultivated bacteria. The objective of this study was to determine the influence of rich media composition on the chemical characteristics of the volatilomes of Staphylococcus aureus and Staphylococcus epidermidis. S. aureus (ATCC 12600) and S. epidermidis (ATCC 12228) were cultured in triplicate in four rich complex media (brain heart infusion (BHI), lysogeny broth (LB), Mueller Hinton broth (MHB), and tryptic soy broth (TSB)), and the volatile metabolites produced by each culture were analyzed using headspace solid-phase microextraction combined with comprehensive two-dimensional gas chromatography—time-of-flight mass spectrometry (HS-SPME-GC×GC-TOFMS). When comparing the chemical compositions of the staph volatilomes by the presence versus absence of volatiles produced in each medium, we observed few differences. However, when the relative abundances of volatiles were included in the analyses, we observed that culturing staph in media containing free glucose (BHI and TSB) resulted in volatilomes dominated by acids and esters (67%). The low-glucose media (LB and MHB) produced ketones in greatest relative abundances, but the volatilome compositions in these two media were highly dissimilar. We conclude that the staphylococcal volatilome is strongly influenced by the nutritional composition of the growth medium, especially the availability of free glucose, which is much more evident when the relative abundances of the volatiles are analyzed, compared to the presence versus absence.

Probing Aggregation Tendencies in Asphaltenes by Gel Permeation Chromatography. Part 2: Online Detection by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Inductively Coupled Plasma Mass Spectrometry

This work is the second installment of a study that probes the aggregation behavior of asphaltenes by gel permeation chromatography (GPC). In part 1, analysis of GPC aggregate fractions collected from the 2017 PetroPhase asphaltene sample by direct infusion revealed an inverse correlation between aggregate size and aromaticity. However, characterization of the largest aggregate fractions by direct infusion was hampered by solvent contaminant peaks and dynamic range limitations due to the extremely low ionization efficiencies of the larger, more aliphatic species that comprise those fractions. Here, we couple the GPC separation with online detection by positive atmospheric pressure photoionization ((+)APPI) 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to overcome those problems and reveal that the most abundant species that comprise the largest aggregate segment are indeed the most aliphatic. The ability to characterize difficult-to-analyze samples, like asphaltenes, is the first major advantage of online coupling. Another benefit is the increased chromatographic resolution afforded by online coupling, which enables a finer examination in the most aggregated region and reveals a local trend opposed to the global trend. The very first species to elute in the largest aggregates were more condensed polyaromatic compounds, and the larger, more aliphatic species elute shortly thereafter in much greater relative abundance.

Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia

BackgroundStenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans, being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans. Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate.ResultsOverall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity.ConclusionsVariation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.

Biosignatures Associated with Freshwater Microbialites.

Freshwater microbialites (i.e., lithifying microbial mats) are quite rare in northern latitudes of the North American continent, with two lakes (Pavilion and Kelly Lakes) of southeastern BC containing a morphological variety of such structures. We investigated Kelly Lake microbialites using carbon isotope systematics, phospholipid fatty acids (PLFAs) and quantitative PCR to obtain biosignatures associated with microbial metabolism. δ13CDIC values (mean δ13CDIC −4.9 ± 1.1‰, n = 8) were not in isotopic equilibrium with the atmosphere; however, they do indicate 13C-depleted inorganic carbon into Kelly Lake. The values of carbonates on microbialite surfaces (δ13C) fell within the range predicted for equilibrium precipitation from ambient lake water δ13CDIC (−2.2 to −5.3‰). Deep microbialites (26 m) had an enriched δ13Ccarb value of −0.3 ± 0.5‰, which is a signature of photoautotrophy. The deeper microbialites (>20 m) had higher biomass estimates (via PLFAs), and a greater relative abundance of cyanobacteria (measured by 16S copies via qPCR). The majority of PLFAs constituted monounsaturated and saturated PLFAs, which is consistent with gram-negative bacteria, including cyanobacteria. The central PLFA δ13C values were highly depleted (−9.3 to −15.7‰) relative to δ13C values of bulk organic matter, suggesting a predominance of photoautotrophy. A heterotrophic signature was also detected via the depleted iso- and anteiso-15:0 lipids (−3.2 to −5.2‰). Based on our carbonate isotopic biosignatures, PLFA, and qPCR measurements, photoautotrophy is enriched in the microbialites of Kelly Lake. This photoautotrophy enrichment is consistent with the microbialites of neighboring Pavilion Lake. This indication of photoautotrophy within Kelly Lake at its deepest depths raises new insights into the limits of measurable carbonate isotopic biosignatures under light and nutrient limitations.

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA

Microorganisms are abundant in the near surface atmosphere and make up a significant fraction of organic aerosols with implications on both human health and ecosystem services. Despite their importance, studies investigating biogeographical patterns of the atmospheric microbiome between urban and suburban areas are limited. Urban and suburban locations (including their microbial communities) vary considerably depending on climate, topography, industrial activities, demographics and other socio-economic factors. Hence, we need more location-specific data to make informed decision affecting air quality, human health, and the implication of a changing climate and policy decisions. The objective of this study was to describe how the atmospheric microbiome varies in composition and function between urban and suburban sites. We used high-throughput sequencing to analyze microbial communities collected at different times from PM2.5 samples collected by active sampling method (using a pump and an impactor) and dust settling of TSP collected by passive sampling method (no pump and no impactor) from an urban and suburban site. We found diverse communities unique in composition at both sites with equivalent functional potential. Taxonomic composition varied significantly with Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Other phyla in greater relative abundance at the urban site. In contrast, Cyanobacteria, Tenericutes, Fusobacteria, and Deinococcus, were enriched at the suburban site. Community diversity also demonstrated a high degree of temporal variation within site. We identified over one-third of the communities as potentially pathogenic taxa (urban: 47.52% ± 14.40%, suburban: 34.53% ± 14.60%) and determined the majority of organisms come from animal-associated host or are environmental non-specific. Potentially pathogenic taxa and source environments were similar between active- and passive- sampling method results. Our research is novel it adds to the underrepresented set of studies on atmospheric microbial structure and function across land types and is the first to compare suburban and urban atmospheric communities.

Effect of alfalfa microbiota on fermentation quality and bacterial community succession in fresh or sterile Napier grass silages

The aim of this study was to reveal the reconstitution dynamics of alfalfa microbiota and their contribution to the fermentation quality of Napier grass silages. Napier grass was harvested at approximately 20% dry matter content, chopped to a theoretical length of cut of 2 to 3 cm, and ensiled in laboratory polyethylene plastic bags (400 × 250 mm) for 30 d. The Napier grass was treated with the following: natural fermentation and distilled water (NG), inoculum of alfalfa microbiota (AM), gamma-ray irradiation and distilled water (IR), and gamma-ray radiation and alfalfa microbiota (IR+AM). Three milliliters of inoculum (containing 8.93 log cfu/mL lactic acid bacteria, 9.76 log cfu/mL Enterobacteriaceae, 5.94 log cfu/mL yeast, and 6.53 log cfu/mL mold) eluted from equivalent fresh alfalfa (450 g) was added to each silo of AM and IR+AM treatments, and 3 mL of distilled water was added to the silo of the NG and IR treatments. Three triplicate silos per treatment were opened on d 1, 3, 5, 7, 14, and 30 for sampling and analysis of fermentation quality and bacterial community. Relative to the NG silages, IR+AM silages exhibited a higher lactic acid concentration. The higher acetic acid concentration in NG than in IR+AM silages after 7 d of ensiling was attributed to the dominant genus of Leuconostoc (64.29-49.04%). Adding alfalfa microbiota to sterile Napier grass could increase ammonia-N concentration compared with NG and IR silages after 3 d of ensiling. Leuconostoc was the most predominant genus in NG silages, followed by Lactobacillus. Pediococcus had a greater relative abundance than the indigenous microorganisms and was exclusively found in AM and IR+AM silages, whereas Lactobacillus exhibited a slight increase after 30 d of ensiling (relative abundance in each silage: 6.29 vs. 3.82%, respectively). Lactobacillus was the predominant genus in IR silages since the onset of the ensiling. These results suggest that alfalfa microbiota affected bacterial community succession in Napier grass silages, which in turn affected the fermentation products. Adding alfalfa microbiota to sterile Napier grass could decrease acetic acid concentration compared with NG silages; however, it increased ammonia-N concentration compared with IR silages after 3 d of ensiling.

Effect of simulated emerald ash borer infestation on nitrogen cycling in black ash (Fraxinus nigra) wetlands in northern Minnesota, USA

Black ash (Fraxinus nigra) wetlands are an important economic, cultural, and ecological resource in the northern Great Lake States, USA, and are threatened by the invasive insect, emerald ash borer (Agrilus planipennis Fairmmaire [EAB]). EAB-induced ash mortality can increase air temperatures, alter understory vegetation communities, and modify wetland hydrology by elevating the water table following canopy dieback, which may, in turn, alter nitrogen cycling in wetland soils and affect plant N uptake, N export to watersheds, and N emissions to the atmosphere. We sampled soils in replicated 1.6-ha plots six years after the following treatments were applied: girdling all ash greater than six cm diameter to simulate EAB-induced mortality, clearcutting with removal of all trees, and an unharvested control. In situ samples were collected from soil cores and from adjacent bulk areas influenced by vegetation to measure the concentration and rates of accumulation of inorganic nitrogen over the 2017 growing season. In the soil cores, the greatest nitrogen accumulation occurred in the unharvested control treatment and nitrate/nitrite were the dominant species of inorganic N. In contrast, in bulk soils, the clearcut treatment had greater overall nitrogen mineralization than both the control and girdle treatments, and ammonium had a greater relative abundance than nitrite/nitrate. Potential N mineralization (assessed with a lab incubation) was not affected by treatment, indicating that treatment effects observed in the field were likely due to changes in the microenvironment. Overall, the effect of simulated EAB on net nitrogen mineralization rates was minimal as mineralization was greatly constrained by ecosystem conditions compared to suitable, laboratory conditions, under which potential N mineralization was an order of magnitude greater than measured in the field. However, canopy treatment influenced water table levels, soil temperature, and vegetation communities, all of which influenced the relative abundance of inorganic N species. Our findings indicate limited indirect effects of EAB on net N mineralization in black ash wetlands.

Similar factors underlie tree abundance in forests in native and alien ranges.

AimAlien plant species can cause severe ecological and economic problems, and therefore attract a lot of research interest in biogeography and related fields. To identify potential future invasive species, we need to better understand the mechanisms underlying the abundances of invasive tree species in their new ranges, and whether these mechanisms differ between their native and alien ranges. Here, we test two hypotheses: that greater relative abundance is promoted by (a) functional difference from locally co‐occurring trees, and (b) higher values than locally co‐occurring trees for traits linked to competitive ability.LocationGlobal.Time periodRecent.Major taxa studiedTrees.MethodsWe combined three global plant databases: sPlot vegetation‐plot database, TRY plant trait database and Global Naturalized Alien Flora (GloNAF) database. We used a hierarchical Bayesian linear regression model to assess the factors associated with variation in local abundance, and how these relationships vary between native and alien ranges and depend on species’ traits.ResultsIn both ranges, species reach highest abundance if they are functionally similar to co‐occurring species, yet are taller and have higher seed mass and wood density than co‐occurring species.Main conclusionsOur results suggest that light limitation leads to strong environmental and biotic filtering, and that it is advantageous to be taller and have denser wood. The striking similarities in abundance between native and alien ranges imply that information from tree species’ native ranges can be used to predict in which habitats introduced species may become dominant.

Oral bacteriome of HIV-1-infected children from Rio de Janeiro, Brazil: Next-generation DNA sequencing analysis.

This study compared the oral bacteriome between HIV-1-infected and non-HIV-1-infected Brazilian children/teenagers. Whole saliva, biofilm from the dorsal surface of the tongue and biofilm from supragingival and subgingival sites were collected from 27 HIV-1-infected and 30 non-HIV-1-infected individuals. Bacterial genomic DNA was extracted and 16S rRNA genes were sequenced using next-generation sequencing technology (Ion Torrent). In the supragingival biofilm, the phylum Firmicutes and genus Streptococcus sp. were more frequent in HIV-1-infected (95% and 78%, respectively) than in non-HIV-1-infected individuals (40% and 24%, respectively). In the subgingival biofilm of HIV-infected participants, the relative abundance of the Veillonella sp. and Prevotella sp. genera were higher than in non-HIV-1-infected participants. On the tongue, the genera with greater relative abundance in HIV-1-infected individuals were Neisseria sp. (21%). In saliva, the difference of the genus Prevotella sp. between non-HIV-1-infected and HIV-1-infected individuals was 15% and 7%, respectively. The Chao index revealed an increase in the richness of both sub- and supragingival biofilms in the HIV-1-infected samples compared with non-HIV-1-infected samples. HIV-1-infected children/teenagers have a higher frequency of the phyla Firmicutes and genus Streptococcus, and their oral microbiome shows more complexity than that of non-HIV-1-infected children/teenagers.

The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection

In this study we examined potential associations of HPV infection with the cervical microbiota. Cervical samples were collected from 87 HIV-seronegative reproductive-age Black South African women. Microbiota were characterized by Illumina sequencing of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. Thirty seven (42.5%) and 30 (34.5%) of the women had prevalent HPV and high-risk (HR)-HPV, respectively. Only 23 women (26.4%) had cervical microbiota dominated by a single Lactobacillus species (L. crispatus (2/87 (2.3%)), L. jensenii (2/87 (2.3%)), and L. iners (19/87 (21.8%)). The majority of the women (56/87 (64.4%)) had diverse cervical microbiota consisting of mainly bacterial vaginosis-associated bacteria. The remaining women (8/87 (9.2%)) had microbiota dominated by Aerococcus, Streptococcus, Chlamydia or Corynebacterium. Women with HR-HPV had significantly higher relative abundances of Aerococcaceae, Pseudomonadaceae and Bifidobacteriaceae compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05, q < 0.2). Gardnerella, Sneathia, and Atopobium were also found at greater relative abundances in HR-HPV-infected women compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05), although the difference was not significant after FDR-adjustment (q > 0.2). Further investigations of the bacterial taxa significantly enriched in HR-HPV-infected women are warranted.

Breastmilk and NICU surfaces are potential sources of fungi for infant mycobiomes

Surfaces within the neonatal intensive care unit (NICU), especially those handled frequently by hospital staff, provide sources of gut-colonizing bacteria for hospitalized infants, in addition to those acquired perinatally from maternal sources such as breastmilk. In comparison to bacteria, very little is known about potential sources of colonizing fungi in the NICU setting. Thus, the objective of this study was to characterize fungal communities (mycobiomes) of potential colonization sources for neonates hospitalized in a large university NICU. We hypothesized that the unit surfaces would contain different mycobiomes than those of human-associated (breastmilk) sources. We characterized mycobiomes of NICU surfaces of multiple individual patient care areas as well as those of breastmilk samples by sequencing the internal transcribed spacer region 2 (ITS2) of the fungal rDNA locus. We found that, across all samples, Candida and Saccharomyces species were the most prevalent taxa and had the greatest relative abundances. Breastmilk samples had significantly higher fungal alpha-diversities than NICU surface samples and fungal community compositions (beta diversities) differed significantly between the two sample types. Mycobiome compositions were predominantly driven by the relative abundances of three fungal taxa: Candida albicans, Candida parapsilosis, and Saccharomyces cerevisiae. In total, 21 individual fungal taxa showed significantly greater relative abundances in breastmilk as compared to NICU surfaces, with three being of particular interest to human health: Candida glabrata, Candida tropicalis, and Cryptococcus neoformans. Since no fungal DNA was detected when whole breastmilk was used as the DNA template, as opposed to breastmilk subjected to cell lysis during the DNA isolation procedure, our results indicate that DNA is from fungal cells and is not cell-free DNA. In summary, both NICU surfaces and human breastmilk harbor distinct fungal communities that could provide a source of fungi for the developing infant gut mycobiota. In particular, Candida and Saccharomyces species are abundant and prevalent for both of these potential sources that infants are exposed to.

Importancia del género Anolis (Lacertilia: Dactyloidae), como indicadores del estado del hábitat, en bosque pluvial tropical del Chocó

El objetivo fue cuantificar el valor de las especies del género Anolis como indicadores ecológicos del estado de conservación de los hábitats usados por estas especies en una zona de bosque tropical en el departamento del Chocó. El método de relevamiento por encuentro visual, fue empleado para establecer especies con mayor abundancia relativa en determinado sitio con distintos grados de cobertura vegetal, el patrón “A” son especies indicadoras de altos niveles de intervención donde se destacó Anolis chloris con el 88.2% de abundancia relativa, patrón “B” se referencia a las especies indicadoras de niveles medios de intervención, donde A. latifrons con el 75% de los individuos fueron registrados en este nivel de tolerancia y el patrón “C”, hace referencia a especies que se encuentran en áreas boscosas con un alto nivel de conservación de su estado natural, donde las especies A. anchicayae (92.8%) y A. notopholis (exclusiva) fueron las más importantes., en cuanto al indice de Valor Indicador Ecológico “IndVal”, se reportaron cuatro especies indicadoras, con una diferencia estadísticamente significativa entre especies; A. anchicayae (IndVal: 92.9%), para áreas de bosque con muchos años de regeneración natural, A. chloris (IndVal: 88.2%), A. maculiventris (IndVal: 65.2%) y A. granuliceps (IndVal: 50.8%). Además, se realizo un análisis de similitud y complementariedad entres las diferentes coberturas, indicando el recambio y la exclusividad de especies entre las mismas y posteriormente se graficaron curvas de rango- abundancia. Los resultados sugerir a los Anolis como grupo indicador del estado de conservación de los bosques tropicales del Chocó.

An assessment of the persistence of pathogenic bacteria removal in chicken manure compost employing clay as additive via meta-genomic analysis.

The aim was to evaluate pathogenic bacteria (PB) survival during the composting of chicken manure (CM) amended with five different dosages of clay compared to CM without clay-applied treatment. The results showed that 85-87% of PB relative abundances (RAs) were significantly reduced in lower dosages of applied clay (T2 and T3). However, the maximum survival of PB was noticed in the T6 and T5 treatments, but most of the PB belong to Firmicutes, Actinobacteria and Proteobacteria phylum and their derivative bacterial species. The changes in PB during the composting were not only strongly influenced by clay amendment but also significantly associated with the succession of bacterial species in compost. Bacillus, Clostridium, Mycobacterium and Klebsiella were the dominant spore-forming bacteria identified in higher dosages of clay (i.e., T4, T5 and T6) treatments, but very low abundance of these bacterial genus and its species were recovered from lower dosages of clay (T2 and T3)-applied treatments. Overall, without clay, amended-CM-derived compost contained a relatively higher PB abundance than other treatments, as the anaerobic bacterial species Clostridium_difficile_AA1, Vibrio_cholerae, and Acinetobacter_calcoaceticus had relatively greater RAs, followed by Klebsiella_oxytoca_10-5248, Paenibacillus_Bacillus_cereus and Bartonella_quintana_RM-11. Thus, CM composting with 4% clay amendment is considered a useful method for the efficient recycling of CM, as this process produced sanitized compost with less survival of PB.

Cetobacterium Is a Major Component of the Microbiome of Giant Amazonian Fish (Arapaima gigas) in Ecuador.

Simple SummaryArapaima gigas is a large, air-breathing, giant fish found in Amazonian rivers, a characteristic that gives this species an advantage in oxygen-deprived waters. It has a very attractive potential for aquaculture in the Amazon region due to its many advantages, including a fast growth rate that approaches 10–15 kg/year. Here, we describe the gut microbiome of Arapaima to understand the potential contribution of this bacterial community to the growth of this fish.Arapaima gigas is a large air-breathing fish found in Amazonian rivers, a characteristic that gives this species an advantage in oxygen-deprived waters. It shows high potential for aquaculture in the Amazon region due to its fast growth rate that approaches 10–15 kg/year. The aim of this study was to explore the composition of the intestinal bacterial community of Arapaima gigas reared in Ecuador using 16S rRNA gene high-throughput sequencing. The analysis revealed significant differences in alpha diversity indices (p < 0.05) and differential distribution of minor components of the intestinal microbiome between small and large fish. However, components with greater relative abundance, such as Cetobacterium, are found in similar proportions.

Evidence of Ash Tree (Fraxinus spp.) Specific Associations with Soil Bacterial Community Structure and Functional Capacity

The spread of the invasive emerald ash borer (EAB) across North America has had enormous impacts on temperate forest ecosystems. The selective removal of ash trees (Fraxinus spp.) has resulted in abnormally large inputs of coarse woody debris and altered forest tree community composition, ultimately affecting a variety of ecosystem processes. The goal of this study was to determine if the presence of ash trees influences soil bacterial communities and/or functions to better understand the impacts of EAB on forest successional dynamics and biogeochemical cycling. Using 16S rRNA amplicon sequencing of soil DNA collected from ash and non-ash plots in central Ohio during the early stages of EAB infestation, we found that bacterial communities in plots with ash differed from those without ash. These differences were largely driven by Acidobacteria, which had a greater relative abundance in non-ash plots. Functional genes required for sulfur cycling, phosphorus cycling, and carbohydrate metabolism (specifically those which breakdown complex sugars to glucose) were estimated to be more abundant in non-ash plots, while nitrogen cycling gene abundance did not differ. This ash-soil microbiome association implies that EAB-induced ash decline may promote belowground successional shifts, altering carbon and nutrient cycling and changing soil properties beyond the effects of litter additions caused by ash mortality.