Total Bacterial Abundance Research Articles

Distribution, community structure and metabolic potential of bacterioplankton in a small boreal lake: Microscopy-based survey and 16S rRNA-based DNA metabarcoding

Bacteria are numerous and diverse organisms that have a significant impact on the functioning of aquatic ecosystems. On the vast territory of the West Siberian Lowland (Russia) there are many rivers, lakes and bogs, the microbial communities of which are almost unexplored. Here, we report the study results on the distribution, diversity, community structure and functions of bacterioplankton in the pelagic and littoral zones of one of the lakes, located in this region (Lake Kuchak) obtained using microscopic techniques and 16S rRNA gene metabarcoding. The high total bacterial abundance and biomass, the diversity indices, and the high number of Actinobacteria amplicon sequence variants (ASVs), along with the relatively low number of Betaproteobacteria ASVs, indicate the eutrophication of the lake, especially in its overgrown littoral zone. Similar bacterial communities developed in the pelagic and littoral zones due to similar environmental conditions in these habitats of this small and shallow lake. Nevertheless, there were some differences between the pelagic and littoral zones, causing differences in the bacterial communities of these zones more in size and morphological structure than in taxonomic composition. Comparative analysis of the bacterial metabolic ways showed the higher functional potential in the pelagic zone compared to the littoral one. Signs of methylotrophic and methanotrophic activities, as well as pollutant biodegradation potential of the bacterioplankton were identified. The bacterial distribution and community composition indicates the input of organic substances into the lake from the watershed, but also shows the community resistance to allochthonous microorganisms. Alpha diversity indices, distribution of taxonomic groups and some other results indicate deterioration of water quality in the overgrown littoral zone.

Microbe-binding Antibodies in the Female Genital Tract: Associations with the Vaginal Microbiome and Genital Immunology.

Bacteria-Ig interactions maintain homeostasis in the gut through the clearance of pathogenic bacteria and the development of immune tolerance to inflammatory bacteria; whether similar interactions modulate inflammation and bacterial colonization in the female genital tract is uncertain. In this study, we used a flow cytometry-based assay to quantify microbe-binding IgA and IgG in the cervicovaginal secretions of 200 HIV-uninfected women from Nairobi, Kenya that were enriched for bacterial vaginosis. Total IgA and IgG were abundant and frequently demonstrated ex vivo binding to the key vaginal bacteria species Gardnerella vaginalis, Prevotella bivia, Lactobacillus iners, and Lactobacillus crispatus, which are largely microbe-specific. Microbe-binding Abs were generally not associated with the presence or abundance of their corresponding bacteria. Total and microbe-binding IgA and IgG were inversely correlated with total bacterial abundance and positively correlated with several proinflammatory cytokines (IL-6, TNF) and chemotactic chemokines (IP-10, MIG, MIP-1α, MIP-1β, MIP-3α, MCP-1, IL-8), independent of total bacterial abundance. Flow cytometry-based quantification of microbe-binding Abs provides a platform to investigate host-microbiota interactions in the female genital tract of human observational and interventional studies. In contrast to the gut, cervicovaginal microbe-binding IgA and IgG do not appear to be immunoregulatory but may indirectly mitigate bacteria-induced inflammation by reducing total bacterial abundance.

The impact of single and combined amendment of elemental sulphur and graphene oxide on soil microbiome and nutrient transformation activities

BackgroundSulphur (S) deficiency has emerged in recent years in European soils due to the decreased occurrence of acid rains. Elemental sulphur (S0) is highly beneficial as a source of S in agriculture, but it must be oxidized to a plant-accessible form. Micro- or nano-formulated S0 may undergo accelerated transformation, as the oxidation rate of S0 indirectly depends on particle size. Graphene oxide (GO) is a 2D-carbon-based nanomaterial with benefits as soil amendment, which could modulate the processes of S0 oxidation. Micro-and nano-sized composites, comprised of S0 and GO, were tested as soil amendments in a pot experiment with unplanted soil to assess their effects on soil microbial biomass, activity, and transformation to sulphates. Fourteen different variants were tested, based on solely added GO, solely added micro- or nano-sized S0 (each in three different doses) and on a combination of all S0 doses with GO. ResultsCompared to unamended soil, nano-S0 and nano-S0+GO increased soil pH(CaCl2). Micro-S0 (at a dose 4 g kg−1) increased soil pH(CaCl2), whereas micro-S0+GO (at a dose 4 g kg−1) decreased soil pH(CaCl2). The total bacterial and ammonium oxidizer microbial abundance decreased due to micro-S0 and nano-S0 amendment, with an indirect dependence on the amended dose. This trend was alleviated by the co-application of GO. Urease activity showed a distinct response to micro-S0+GO (decreased value) and nano-S0+GO amendment (increased value). Arylsulfatase was enhanced by micro-S0+GO, while sulphur reducing bacteria (dsr) increased proliferation due to high micro-S0 and nano-S0, and co-amendment of both with GO. In comparison to nano-S0, the amendment of micro-S0+GO more increased soluble sulphur content more significantly. ConclusionsUnder the conditions of this soil experiment, graphene oxide exhibited a significant effect on the process of sulphur oxidation.

Continental-scale insights into the sugarbeet diffusion juice microbiomes.

Bacterial contamination of raw diffusion juice poses unique challenges during the sugar extraction process. This study profiled bacterial communities by using full-length 16S rRNA amplicon sequencing and quantified the carbohydrate concentrations in raw diffusion juice samples received from sugar factory regions across the USA and Canada. Juice samples were collected at four time points during the 2021 and 2022 processing campaigns. Firmicutes was the dominant phylum from the raw diffusion juice samples collected during both campaigns and comprised 85.5% of total bacterial abundance. Lactic acid bacteria such as Leuconostoc and Lactobacillus were among the core genera which also dominated the bacterial community in raw diffusion juice. Positive correlations in the abundance of functionally and taxonomically related bacterial communities were identified. During the 2021 campaign, 44 bacterial genera were differentially abundant in raw diffusion juice extracted from sugarbeet roots in Periods 1 to 4. This number declined sixfold during the 2022 campaign to three genera. The concentration of raffinose in raw diffusion juice positively correlated to the relative abundance of Leuconostoc. Furthermore, an in vitro assay was performed to assess the growth dynamics of Leuconostoc mesenteroides in sucrose or raffinose-rich medium and observed the rapid consumption of both carbohydrates by this bacterium. This finding is important for deciphering microbial growth dynamics in raw diffusion juice that can be useful in minimizing sugar loss during the factory processing.IMPORTANCEFindings additionally provide baseline information that can be used to develop mitigation strategies that reduce losses due to microbial contamination of sucrose processing streams.

PSI-22 Evaluating colonization success of Bacteroidetes from different host origin in broiler chickens

Abstract Current broiler production practices that aim to maximize biosecurity have limited chick exposure to beneficial microbes. Previous research highlights a notable disparity in Bacteroidetes abundance and taxonomy between birds reared under intensive and extensive systems. Building upon this, we hypothesized that Bacteroidetes strains populating intensively raised birds may originate from human sources, potentially leading to varied colonization efficiencies. The objective of this study was to evaluate the colonization patterns of diverse Bacteroidetes strains within the chicken gastrointestinal tract. One day-old broiler birds (n = 63) were raised in individually ventilated isolators accommodating 3 birds per cage. The chicks were subjected to inoculation either via oral gavage with 150 µL of glycerol stock containing 1x104 colony forming units (CFU)/mL; or spray method (2 mL per cage) using chicken-derived, human-derived, and a combination of Bacteroidetes strains. Notably, birds administered via oral gavage displayed an increase in body weight gain by d 07 compared with their counterparts treated via spray and the control group (P < 0.01). Subsequent quantification of Bacteroidetes, Enterobacteriaceae, and total bacteria using qPCR revealed that oral gavage resulted in more successful Bacteroidetes colonization at d 14 (P < 0.01). Moreover, discernible variations were noted in total bacterial abundance across treatment cohorts. It can be concluded that the method of inoculation appears to influence the initial colonization patterns of Bacteroidetes in the chicken gut, or that inoculation in the environment requires a higher dose. Amplicon sequencing that is underway will reveal the success of the Bacteroidetes from different host origin and the most successful strains of chicken origin. Overall, enhanced growth coincided with more successful Bacteroidetes colonization, identifying them as potential targets for enhanced broiler performance. Further investigation is warranted to determine if Bacteroidetes from different sources demonstrate varying colonization efficiencies.

Cystic fibrosis pathogens persist in the upper respiratory tract following initiation of elexacaftor/tezacaftor/ivacaftor therapy.

Elexacaftor/tezacaftor/ivacaftor (ETI) therapy has revolutionized the treatment of cystic fibrosis (CF) for most affected individuals but the effects of treatment on sinus microbiota are still unknown. Changes to the airway microbiota in CF are associated with disease state and alterations to the bacterial community after ETI initiation may require changes to clinical management regimens. We collected sinus swab samples from the middle meatus in an observational study of 38 adults with CF and chronic rhinosinusitis (CRS) from 2017 to 2021 and captured the initiation of ETI therapy. We performed 16S and custom amplicon sequencing to characterize the sinus microbiota pre- and post-ETI. Real-time quantitative PCR (RT-qPCR) was performed to estimate total bacterial abundance. Sinus samples from people with CF (pwCF) clustered into three community types, dependent on the dominant bacterial organism: a Pseudomonas-dominant, Staphylococcus-dominant, and mixed dominance cluster. Shannon's diversity index was low and not significantly altered post-ETI. Total bacterial load was not significantly lowered post-ETI. Pseudomonas spp. abundance was significantly reduced post-ETI, but eradication was not observed. Staphylococcus spp. became the dominant organism in most individuals post-ETI and we showed the presence of methicillin-resistant Staphylococcus aureus (MRSA) in the sinus both pre- and post-ETI. We also demonstrated that the sinus microbiome is predictive of the presence of Pseudomonas spp., Staphylococcus spp., and Serratia spp. in the sputum. Pseudomonas spp. and Staphylococcus spp., including MRSA, persist in the sinuses of pwCF after ETI therapy, indicating that these pathogens will continue to be important in CF airway disease management in the era of highly effective modulator therapies (HEMT).IMPORTANCEHighly effective modulator therapies (HEMT), such as elexacaftor/tezacaftor/ivacaftor (ETI), for cystic fibrosis (CF) have revolutionized patient care and quality of life for most affected individuals. The effects of these therapies on the microbiota of the airways are still unclear, though work has already been published on changes to microbiota in the sputum. Our study presents evidence for reduced relative abundance of Pseudomonas spp. in the sinuses following ETI therapy. We also show that Staphylococcus spp. becomes the dominant organism in the sinus communities of most individuals in this cohort after ETI therapy. We identified methicillin-resistant Staphylococcus aureus (MRSA) in the sinus microbiota both pre- and post-therapy. These findings demonstrate that pathogen monitoring and treatment will remain a vital part of airway disease management for people with cystic fibrosis (pwCF) in the era of HEMT.

Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial

BackgroundTranslational microbiome research using next-generation DNA sequencing is challenging due to the semi-qualitative nature of relative abundance data. A novel method for quantitative analysis was applied in this 12-week clinical trial to understand the mechanical vs. chemotherapeutic actions of brushing, flossing, and mouthrinsing against the supragingival dental plaque microbiome. Enumeration of viable bacteria using vPCR was also applied on supragingival plaque for validation and on subgingival plaque to evaluate interventional effects below the gingival margin.MethodsSubjects with gingivitis were enrolled in a single center, examiner-blind, virtually supervised, parallel group controlled clinical trial. Subjects with gingivitis were randomized into brushing only (B); brushing and flossing (BF); brushing and rinsing with Listerine® Cool Mint® Antiseptic (BA); brushing and rinsing with Listerine® Cool Mint® Zero (BZ); or brushing, flossing, and rinsing with Listerine® Cool Mint® Zero (BFZ). All subjects brushed twice daily for 1 min with a sodium monofluorophosphate toothpaste and a soft-bristled toothbrush. Subjects who flossed used unflavored waxed dental floss once daily. Subjects assigned to mouthrinses rinsed twice daily. Plaque specimens were collected at the baseline visit and after 4 and 12 weeks of intervention. Bacterial cell number quantification was achieved by adding reference amounts of DNA controls to plaque samples prior to DNA extraction, followed by shallow shotgun metagenome sequencing.Results286 subjects completed the trial. The metagenomic data for supragingival plaque showed significant reductions in Shannon-Weaver diversity, species richness, and total and categorical bacterial abundances (commensal, gingivitis, and malodor) after 4 and 12 weeks for the BA, BZ, and BFZ groups compared to the B group, while no significant differences were observed between the B and BF groups. Supragingival plaque vPCR further validated these results, and subgingival plaque vPCR demonstrated significant efficacy for the BFZ intervention only.ConclusionsThis publication reports on a successful application of a quantitative method of microbiome analysis in a clinical trial demonstrating the sustained and superior efficacy of essential oil mouthrinses at controlling dental plaque compared to mechanical methods. The quantitative microbiological data in this trial also reinforce the safety and mechanism of action of EO mouthrinses against plaque microbial ecology and highlights the importance of elevating EO mouthrinsing as an integral part of an oral hygiene regimen.Trial registrationThe trial was registered on ClinicalTrials.gov on 31/10/2022. The registration number is NCT05600231.

Heterogeneous Antibiotic Resistance Gene Removal Impedes Evaluation of Constructed Wetlands for Effective Greywater Treatment.

Microorganisms carrying antimicrobial resistance genes are often found in greywater. As the reuse of greywater becomes increasingly needed, it is imperative to determine how greywater treatment impacts antimicrobial resistance genes (ARGs). Using qPCR and SmartChip™ qPCR, we characterized ARG patterns in greywater microbial communities before, during, and after treatment by a recirculating vertical flow constructed wetland. In parallel, we examined the impact of greywater-treated irrigation on soil, including the occurrence of emerging micropollutants and the taxonomic and ARG compositions of microbial communities. Most ARGs in raw greywater are removed efficiently during the winter season, while some ARGs in the effluents increase in summer. SmartChip™ qPCR revealed the presence of ARGs, such as tetracycline and beta-lactam resistance genes, in both raw and treated greywater, but most abundantly in the filter bed. It also showed that aminoglycoside and vancomycin gene abundances significantly increased after treatment. In the irrigated soil, the type of water (potable or treated greywater) had no specific impact on the total bacterial abundance (16S rRNA gene). No overlapping ARGs were found between treated greywater and greywater-irrigated soil. This study indicates ARG abundance and richness increased after treatment, possibly due to the concentration effects of the filter beds.

Dissolved carbohydrates and its influence on bacterioplankton diversity in the euphotic zone of Equatorial Indian Ocean during southwest monsoon

The Equatorial Indian Ocean (EIO) is oligotrophic in nature, low in productivity and characterised by relatively high bacterial biomass and heterotrophic productivity. The microbial biomass is fuelled by dissolved organic carbon (DOC) whose lability depends upon its chemistry. During an expedition in the EIO, samples for dissolved carbohydrates (DCHO), dissolved monosaccharide (MCHO), dissolved polysaccharide (PCHO), total bacterial abundance, total organic carbon (TOC), nutrients, chlorophyll a (chl a), bacterial diversity, and phytoplankton composition were estimated along two transects (TS-1 & TS-2) in the euphotic depth (200 m). DCHO and MCHO samples were analysed using 3-methyl-2-benzothiozolinone hydrazone hydrochloride (MBTH) method. The DCHO, MCHO, and PCHO concentrations in TS-1 ranged from 2.4 to 5.8 μM; 0.7 to 2.7 μM; 0.7 to 3.4 μM, while in TS-2 it ranged from 2.2 to 4.8 μM; 0.3 to 2.8 μM; 0.2 to 3.8 μM, respectively. Vertically, DCHO concentrations decreased within the photic depths in most stations. PCHO concentrations were relatively greater in TS-2 than TS-1, which may be due to preferential removal of MCHO in TS-2. In the top 200 m of the water column, Proteobacteria was the most abundant bacterial phylum followed by Cyanobacteria, Actinobacteriota, Bacteroidota, and SAR-324 while dinoflagellates dominated the phytoplankton population. The distribution of DCHO and PCHO were inversely correlated to salinity, temperature, and chl a. The bacterial heterotrophs like alpha-Proteobacteria, Chloroflexii, and Verrumicrobiota along with SAR324 and Actinobacteriota were clustered with nutrients, while Bdellovibriota and Dadabacteria clustered with MCHO, PCHO, and DCHO. These results highlight the impact of DCHO & PCHO lability on the distribution of bacterial community and delineate oceanographic factors that regulate the distribution of DCHO and its constituents in EIO waters.

Microbiome comparisons reveal the core microorganisms and key nitrogen metabolic pathway involved in industrial nitrogen fertilizer wastewater treatment plants

Microbiomes from municipal wastewater treatment plants (WWTPs) have been widely investigated, but less attention has been paid to those in the industrial WWTPs. To compare the microbiomes involved in nitrogen fertilizer wastewater treatment, four WWTPs with different concentrations and types of pollutants, processes, and geographic locations were chosen. Diversity results revealed that microbial community was similar within the same WWTP, but different among the four WWTPs. CPCoA further demonstrated these differences (P = 0.022), implying that the diverse manufactured products acted as electron donors to create distinct ecological niches for denitrification. However, bacterial composition and functional profile were similar among four WWTPs (P > 0.05), and their abundance differed and fluctuated. More than 80 % of the dominant genera detected were present in all four WWTPs. And the core bacteria identified were Hyphomicrobium, Acinetobacter, Pedomicrobium, Methyloversatilis, Gp16, Thauera, and Moorella respectively, accounting for 19.524 % of total bacterial abundance. Forty-five nitrogen metabolism genes were active in four nitrogen cycle pathways (nitrification, assimilatory nitrate reduction, dissimilatory nitrate reduction, denitrification). The key genes were amoC (0.30 %), nasA (5.35 %), nirA (2.17 %), nirB (6.04 %), nirD (5.82 %), narG (3.87 %), narH (4.65 %), nirK (3.90 %), norB (3.32 %), nosZ (2.80 %). Hyphomicrobium, Thauera, Afipia, and Paracocccus were the hosts of denitrification genes, synergistically treating the nitrogen fertilizer wastewater to meet the discharge standard. These results suggested that microbial community structure in the nitrogen fertilizer industry is similar, helping further the understanding of the microbiota at an industry level though more samples are required to verify this.

Temporal patterns of bacterial communities in the Billings Reservoir system

In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO4–2), phosphate (P), ammonia (NH3), and nitrate (NO3-) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH3 are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.

Weakened pelagic-benthic coupling on an Arctic outflow shelf (Northeast Greenland) suggested by benthic ecosystem changes

Arctic marine ecosystems are becoming more boreal due to climate change. Predictions of ecosystem change focus mainly on Arctic inflow or interior shelves, with few comprehensive studies on Arctic outflow regions. During September–October 2017, soft-bottom communities were sampled and benthic ecosystem processes were quantified at 12 stations on the Northeast Greenland shelf (outflow shelf) and compared to the last regional ecosystem study, conducted in 1992 and 1993. The benthic habitat was characterized in terms of sediment granulometry, pigment concentrations, and porewater chemistry (dissolved inorganic carbon, nutrients). Total abundance and biomass of macrobenthos and meiobenthos, bacterial abundance, porewater dissolved inorganic carbon and ammonium concentrations were higher on the outer shelf compared to locations adjacent to the Nioghalvfjerdsfjorden glacier at 79°N and the inner shelf stations (e.g., macrofauna: 1,964–2,952 vs. 18–1,381 individuals m−2). These results suggest higher benthic production in the outer parts of the NEG shelf. This difference was also pronounced in macrobenthic and meiobenthic community structure, which was driven mainly by food availability (pigments with 1.3–4.3 vs. 0.3–0.9 µg g−1 sediment, higher total organic carbon content and bacterial abundance). Compared to the early 1990s, warmer bottom water temperatures, increased number of sea-ice-free days and lower sediment pigment concentrations in 2017 were accompanied by decreased polychaete and increased nematode abundance and diversity, and a different community structure of nematode genera. The present study confirms previous reports of strong pelagic-benthic coupling on the NEG shelf, but highlights a possible weakening since the early 1990s, with a potential shift in importance from macrofauna to meiofauna in the benthic community. Increasing inflow of Atlantic water and decreasing volume transport and thickness of sea ice through the Fram Strait, probably affecting the Northeast Water Polynya, may be responsible, suggesting ecosystem-wide consequences of continued changes in sea-ice patterns on Arctic shelves.

The spatial and temporal effect of electrochromic windows on indoor and human microbiome in an inpatient hospital.

Improving the hospital environment and developing novel disinfection strategies are critical for infection control in healthcare settings. In this study, we explored the effects of electrochromic (EC) windows on indoor and patient microbiome in an inpatient hospital. Hematology-Oncology patients at the University of Vermont Medical Center. We conducted a prospective study in ten occupied patient rooms. Five of the patient rooms had active EC windows that tint dynamically to control for heat and glare, and the other five rooms had deactivated EC windows that simulated traditional windows and blinds. Samples were collected one day before patient admission as baseline and on the 1st, 3rd, and 5th day of the patient stay. Total bacterial abundance and bacterial community structure were determined through quantitative PCR and 16s rRNA Illumina MiSeq sequencing, respectively. Patient rooms with active EC windows had significantly lower light intensity and temperature than traditional patient rooms with blinds. The absolute bacterial abundance and diversities on windows were significantly lower in rooms with EC windows and the bacterial composition changed after one day EC window activation. Compared to baseline, relative abundance of the Staphylococcus genus was significantly lower on EC window surface during the five-day experiment. In contrast, the air microbiome was more diverse in rooms with EC windows. Active electrochromic (EC) windows in patient rooms result in lower light intensity and temperature, reduced bacterial abundance and diversities on window surfaces, and a more diverse air microbiome, informing future healthcare design.

The terroir of Tempeh: Strong region-specific signatures in the bacterial community structures across Indonesia

Tempeh, a soybean product from Indonesia, is created through fermentation by Rhizopus spp. and associated bacteria. Here, we aim to get an overview of the variability of the tempeh microbiota across Indonesia and disentangle influencing factors. We found high variability in bacterial abundance (103 – 109 copies g-1), richness (nASV = 40 – 175 ASVs), and diversity (H’ = 0.9 – 3.5) in tempeh. The primary factor affecting this variation was the region, where the tempeh was produced. Interestingly, tempeh samples obtained from geographically close areas tended to share similar bacterial profiles, suggesting a "terroir" of tempeh. Additionally, tempeh wrapped in banana leaves had a higher abundance of enterobacteria in comparison to tempeh wrapped in plastic but also tended to have a higher total bacterial and lactobacilli abundance. Despite all variability, the tempeh core microbiome consists Lactobacillales and Enterobacteriales. This study demonstrates a high variability of bacterial diversity in traditional tempeh from local producers highlighting a strong regional influence across Indonesia.

66 Whole-Body Biogeography of the Bacterial Microbiota in Newborn Calves and Response of These Communities to Prenatal Vitamin and Mineral Supplementation

Abstract During gestation, alterations in maternal nutrition during fetal development may alter growth trajectory and metabolic function in the developing fetus. Additionally, there is increasing evidence that the fetal microbiome also influences developmental outcomes. Research in this area is limited, and gastrointestinal microbiota has been the primary focus in cattle. Our objective was to assess the whole-body biogeography of the newborn calf microbiota and the response of these microbial communities and the calf immune system to prenatal vitamin and mineral (VTM) supplementation. Samples were collected from the hoof, liver, lung, nasal cavity, eye, rumen (tissue and fluid), and vagina of female beef calves that were born from dams that received either prenatal VTM or no VTM (Control; n = 7/group) throughout gestation. Calves were separated from their dams immediately after birth and fed colostrum replacement until euthanasia at 30 h post-initial colostrum feeding. The microbiota from swab and tissue samples were assessed using 16S rRNA gene sequencing (V4) and qPCR. Serum samples were processed for multiplex quantification of 15 cytokines and chemokines. Sequencing revealed the presence of a relatively diverse and complex microbiota in each of the 7 anatomical locations. The community structure of the hoof, liver, ocular, and vaginal microbiota were significantly different from the ruminal microbiota (0.64 ≥ R2 ≥ 0.12, P ≤ 0.003). The respiratory (nasal and lung) had similar community structures to that of ocular, vaginal, and ruminal fluid microbiota (P &amp;gt; 0.11). The ocular, hoof, and vagina had the greatest microbial richness (observed ASVs; P &amp;lt; 0.05) but similar diversity (Shannon; P &amp;gt; 0.05) compared with other samples. The liver and ruminal fluid had the least microbially rich communities, the latter also being the least diverse (P &amp;lt; 0.05). Firmicutes, Actinobacteriota, and Proteobacteria were the dominant phyla across all sample types, but their abundance varied by location. The ruminal fluid and hoof had the greatest bacterial concentration, while the liver, lung and ruminal tissue had reduced bacterial abundance as estimated by qPCR. An influence of VTM supplementation on microbial community structure was only detected in the ruminal fluid microbiota (P &amp;lt; 0.01). While prenatal VTM supplementation did not affect the nasal, lung, liver, and hoof microbiota, differences (P &amp;lt; 0.05) were detected in microbial richness (vagina), diversity (ruminal tissue and fluid, ocular), composition at the phylum level (ruminal tissue, ocular, and vagina), and total bacterial abundance (ocular and vagina). Among the 15 cytokines evaluated, the concentration of IP-10 was increased (P = 0.02) while IL-4 and IL-17A were reduced (P &amp;lt; 0.05)

Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection

BackgroundTobramycin inhalation solution (TIS) and chronic azithromycin (AZ) have known clinical benefits for children with CF, likely due to antimicrobial and anti-inflammatory activity. The effects of chronic AZ in combination with TIS on the airway microbiome have not been extensively investigated. Oropharyngeal swab samples were collected in the OPTIMIZE multicenter, randomized, placebo-controlled trial examining the addition of AZ to TIS in 198 children with CF and early P. aeruginosa infection. Bacterial small subunit rRNA gene community profiles were determined. The effects of TIS and AZ were assessed on oropharyngeal microbial diversity and composition to uncover whether effects on the bacterial community may be a mechanism of action related to the observed changes in clinical outcomes.ResultsSubstantial changes in bacterial communities (total bacterial load, diversity and relative abundance of specific taxa) were observed by week 3 of TIS treatment for both the AZ and placebo groups. On average, these shifts were due to changes in non-traditional CF taxa that were not sustained at the later study visits (weeks 13 and 26). Bacterial community measures did not differ between the AZ and placebo groups.ConclusionsThis study provides further evidence that the mechanism for AZ’s effect on clinical outcomes is not due solely to action on airway microbial composition.

Organic fertilizer and hydrothermal conditions change the distribution of Medicago sativa L. productivity and soil bacterial diversity in coastal saline soil

BackgroundAlfalfa (Medicago sativa L.) is a perennial leguminous forage that can improve the properties of saline soil. In addition, the supplementation with fertilizer to promote soil bacterial activity is critical to improve the productivity of coastal saline soils. However, the association between fertilizer application, bacterial community characteristics, and alfalfa yield in saline soil remains unclear.AimTo understand the interaction of different fertilizer and environmental factors on soil bacterial diversity and alfalfa yield in coastal saline soil.ResultsA 4-year field study was conducted to examine the interaction of different fertilizer treatments and environmental factors on soil bacterial diversity and alfalfa yield in coastal saline soil in China. Three organic fertilizer treatments (fulvic acid potassium, fulvic acid potassium + wood vinegar, and fulvic acid potassium + Bacillus), one biochar treatment (bio-charcoal), one inorganic fertilizer treatment (diammonium phosphate), and a control (no fertilizer) were included. The effects of the six treatments and 15 cutting times on alfalfa yield and soil bacterial community diversity were assessed. The productivity in fulvic acid potassium + Bacillus and fulvic acid potassium treatments was 68.37 and 67.90 t·hm−2 in 4 years, which was significantly higher than that in the bio-charcoal treatment and control. Hydrothermal conditions and timing of alfalfa harvest had significant effects on the soil bacterial community. Proteobacteria, Acidobacteria, and Actinobacteria were the principal bacterial phyla detected in the soil samples, collectively accounting for approximately 60% of the total bacterial abundance. The relative abundance of Bacteroidetes, Firmicutes, and Nitrospirae was significantly correlated with alfalfa yield, and the abundance of these phyla was also affected by the maximum temperature and precipitation. Fertilizer supplementation in coastal saline soil can effectively increase the yield of alfalfa. Among the fertilizers tested, fulvic acid potassium had the strongest effect, whereas bio-charcoal fertilizer had little effect on alfalfa yield.Graphical

Biological denitrification inhibition (BDI) on nine contrasting soils: An unexpected link with the initial soil denitrifying community

Denitrification is considered the major pathway leading to soil gaseous (N) losses, affecting N availability for plants and consequently plant productivity. Biological denitrification inhibition (BDI) in Fallopia spp., a plant species complex with a high level of growth and competitiveness for mineral N, acts through procyanidin production. However, the soil factors governing BDI development are still unknown. Through a mesocosm experiment using two treatments – soil planted with Fallopia japonica and unplanted–, nine biologically and physically contrasting soils were studied with the aim to ascertain how each can affect BDI development. Microbial enzyme activities (respiration - SIR, denitrification - DEA), denitrifying functional gene abundance (nirK, nirS), total bacterial community abundance (rRNA 16S) and soil physicochemical parameters (N mineral forms, soil texture, moisture, pH) were measured before and after plant growth, and the DEA:SIR ratio was used as a BDI proxy. The DEA:SIR ratio decreased for six soils. BDI development is related to a small number of soil factors, mainly initial soil moisture and ammonium concentration, and unexpectedly, with the initial abundance of nirK(in), nirS(in) and rRNA 16S(in). The intensity of this decrease is positively correlated to the level of DEA in unplanted soil: the higher the DEA in unplanted soil, the more intense the BDI under F. japonica. The procyanidin concentration of the F. japonica belowground system was positively correlated to BDI intensity. These results suggest that a procyanidin assay from the plant belowground system could be a new proxy for measuring BDI intensity. Interestingly, this research shows that BDI is not systematic, and that few (a)biotic soil parameters influence its development. More importantly, this research is the first to highlight that biotic factors are relevant in explaining BDI. This paper also presents new perspectives on plant-microorganism interactions in terms of plant awareness of the soil microbial community.

Analysis on the pharyngeal microbiota in patients with laryngopharyngeal reflux disease

Objective(s)In this study, the laryngopharynx microbiome alterations were characterized after proton pump inhibitor treatment in patients with Laryngopharyngeal Reflux Disease (LPRD) and healthy people. The potential outcome-predictive biomarker was explored. MethodsPatients with LPRD and healthy controls were enrolled. The composition of their laryngopharynx microbiota was analyzed both by traditional plate count of the main bacterial groups and PCR amplification followed by denaturing gradient gel electrophoresis. Shannon-Wiener index and evenness index based on Dice index were used to assess the bacterial diversity. Droplet digital PCR was used to determine the total bacterial RNA and relative abundance of Klebsiella oxytoca. Receiver operating characteristic curve was plotted to explore the potential of Klebsiella oxytoca as an outcome-predictive biomarker. ResultsA total of 29 LPRD cases and 28 healthy subjects were enrolled. The composition of the laryngopharynx microbiota was almost similar, except Klebsiella oxytoca. The cluster analysis showed that the similarity between healthy and treatment-effective groups, as well as pretreatment and treatment-invalid groups, was close. Statistical analysis showed that there were differences in the diversity index and richness among the healthy, treatment-effective, pretreatment and treatment-invalid groups. The abundance of Klebsiella oxytoca in the treatment-effective LPRD group was lower than that of the treatment-invalid LPRD group. The abundance of Klebsiella oxytoca can distinguish treatment-effective and -invalid groups (AUC=0.859) with a sensitivity of 77.78% and specificity of 90.91%. ConclusionThere were differences in the diversity of cecal contents microbial community between treatment-invalid and treatment-effective LPRD groups. Klebsiella oxytoca has potential to distinguish treatment outcomes. Level of evidenceHow common is the problem? Level 1. Is this diagnostic or monitoring test accurate? (Diagnosis) Level 4. What will happen if we do not add a therapy? (Prognosis) Level 5. Does this intervention help? (Treatment Benefits) Level 4. What are the COMMON harms? (Treatment Harms) Level 4. What are the RARE harms? (Treatment Harms) Level 4. Is this (early detection) test worthwhile?(Screening) Level 4.

The voltage-gated sodium channel, para, limits Anopheles coluzzii vector competence in a microbiota dependent manner

The voltage-gated sodium channel, para, is a target of DDT and pyrethroid class insecticides. Single nucleotide mutations in para, called knockdown resistant or kdr, which contribute to resistance against DDT and pyrethroid insecticides, have been correlated with increased susceptibility of Anopheles to the human malaria parasite Plasmodium falciparum. However, a direct role of para activity on Plasmodium infection has not yet been established. Here, using RNA-mediated silencing, we provide in vivo direct evidence for the requirement of wild-type (wt) para function for insecticide activity of deltamethrin. Depletion of wt para, which is susceptible to insecticide, causes deltamethrin tolerance, indicating that insecticide-resistant kdr alleles are likely phenocopies of loss of para function. We then show that normal para activity in An. coluzzii limits Plasmodium infection prevalence for both P. falciparum and P. berghei. A transcriptomic analysis revealed that para activity does not modulate the expression of immune genes. However, loss of para function led to enteric dysbiosis with a significant increase in the total bacterial abundance, and we show that para function limiting Plasmodium infection is microbiota dependent. In the context of the bidirectional “enteric microbiota-brain” axis studied in mammals, these results pave the way for studying whether the activity of the nervous system could control Anopheles vector competence.