Microbial Relative Abundance Research Articles

(024) A Randomized Trial on the Sexual Effectiveness and Impact on the Vaginal Microbiome of Reformulated Personal Water Lubricants with Lowered Osmolality and pH in Premenopausal and Postmenopausal Women

Abstract Introduction Vaginal dryness may be associated with postmenopausal women; however, it may also occur due to chronic medical conditions and as a direct side effect from medications. Personal lubricants can address sexual complaints and symptomatology associated with vaginal dryness, although clinically published data supporting their efficacy remains limited. Age-associated vaginal-physiological changes due to hypoestrogenic milieux include increased pH, decreased natural lubrication, reduced endothelial rugae and altered vaginal microbiome. While personal lubricants may alleviate symptoms, their definitive effects on the vaginal microbiome remain understudied and underappreciated. Objective This study examined reformulated water-based lubricants (lowered osmolalities and pH,) and their effect on female sexual function compared to their counterparts (higher osmolalities/increased pH). A secondary analysis examined if these reformulated lubricants influenced the vaginal microbiome of women from different age groups. Methods An open-label, parallel-design study was performed in heterosexual women in stable monogamous relationships, aged 18–65 years with mild-to-moderate vaginal dryness and dyspareunia. The study population (n=174) included an approximate 50:50 ratio of premenopausal to postmenopausal women. The randomization schedule was stratified by menopausal status. Subjects were randomized to use one of five water-based lubricants and instructed to use their lubricant during vaginal intercourse at least once a week over a 4-week period. The Female Sexual Function Index (FSFI) measured sexual functioning after 4 weeks of use as an indicator of lubricant performance. More than a 4-point increase in total FSFI is deemed clinically important. From the study-enrolled subjects, 50 females were randomized to one of five lubricant treatment groups for secondary microbiome analysis. To this end, four vaginal swabs per participant were sampled during pre- (“baseline”) and post- (“2 hours”, “24 hours” and “4 weeks”) lubricant application to assess bacterial diversity via 16S sequencing. Additionally, vaginal moisture and pH measurements were collected at baseline, 2 hours, and 24 hours post-lubricant application and correlated with microbiome diversity and richness using non-parametric tests and linear mixed models. Results An increase in FSFI total score of >4 points was found for all lubricants in the total population and for 4/5 lubricants in the premenopausal subgroup, as indicated by the mean differences to baseline. The number of subjects in sexual function (total FSFI >26.55) after treatment was significantly greater than the number in sexual function before treatment for both subgroups (premenopausal 19.3% to 78.4%; postmenopausal 22.3% to 75.3%; p<0.0001 for both). Lactobacillus species and Gardnerella vaginalis were the predominant taxa across all participants. Repeated lubricant applications did not alter the vaginal microbiome for up to 4 weeks post-product applications. Microbial diversity and relative abundance differed significantly between age groups but remained unaffected during product applications. Relative abundance of Lactobacilli spp. negatively correlated with vaginal pH while that of Gardnerella spp. showed a positive correlation with vaginal pH across all age groups. Conclusions These reformulated lubricants can be used not only to relieve symptomatology of vaginal dryness and dyspareunia, but to enhance overall sexual satisfaction regardless of menopausal status. These study lubricants demonstrated no significant impact on vaginal microbiome. Further studies with larger samples are warranted. Disclosure Yes, this is sponsored by industry/sponsor: Reckitt Benckiser Health. Clarification: Industry funding only - investigator initiated and executed study. Any of the authors act as a consultant, employee or shareholder of an industry for: Reckitt Benckiser Health.

Microbiota in the oral cavity of school-age children with HIV who started antiretroviral therapy at young ages in South Africa.

Infancy is an important developmental period when the microbiome is shaped. We hypothesized that earlier antiretroviral therapy (ART) initiation would attenuate HIV effects on microbiota in the mouth. Oral swabs were collected from 477 children with HIV (CWH) and 123 children without (controls) at two sites in Johannesburg, South Africa. CWH had started ART less than 3 years of age; 63% less than 6 months of age. Most were well controlled on ART at median age 11 years when the swab was collected. Controls were age-matched and recruited from the same communities. Sequencing of V4 amplicon of 16S rRNA was done. Differences in microbial diversity and relative abundances of taxa were compared between the groups. CWH had lower alpha diversity than controls. Genus-level abundances of Granulicatella, Streptococcus, and Gemella were greater and Neisseria and Haemophilus less abundant among CWH than controls. Associations were stronger among boys. Associations were not attenuated with earlier ART initiation. Shifts in genus-level taxa abundances in CWH relative to controls were most marked in children on lopinavir/ritonavir regimens, with fewer shifts seen if on efavirenz ART regimens. A distinct profile of less diverse oral bacterial taxa was observed in school-aged CWH on ART compared with uninfected controls suggesting modulation of microbiota in the mouth by HIV and/or its treatments. Earlier ART initiation was not associated with microbiota profile. Proximal factors, including current ART regimen, were associated with contemporaneous profile of oral microbiota and may have masked associations with distal factors such as age at ART initiation.

Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods

The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R2 = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R2 = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.

Inoculations of phosphate-solubilizing bacteria alter soil microbial community and improve phosphorus bioavailability for moso bamboo (Phyllostachys edulis) growth

Moso bamboo plantations suffer from phosphorus (P) limitations. A better understanding of soil P cycling contributes to the sustainable management and development of the bamboo forests. In this study, different phosphate-solubilizing bacteria (PSB) were applied to soils to stimulate bamboo growth, and the metagenomics method was employed to investigate the changes in soil microbial communities and relative abundances of functional genes. Meanwhile, soil properties and bamboo biomass and physiological indices were also quantitatively analyzed. The PSB inoculations changed soil P fractions and significantly elevated available P (AP) content by stimulating phosphatase activity and functional genes involved in P-transformation. The PSB inoculations significantly stimulated soil acid phosphatase activities and enhanced the relative abundances of functional genes associated with inorganic P-solubilization and organic P-mineralization. Moreover, increased soil available nutrients were beneficial to the moso bamboo growth, and the bamboo biomass in the different treatments increased by from 32.43 % to 69.04 % compared with the control treatment. Significant increases in root activity, carotenoid, chlorophyll a and total chlorophyll contents after the PSB inoculations also contributed to moso bamboo growth. The PSB strain inoculations shaped soil microbial communities and increased microbial connections. Besides adjusting soil P supplies and functional genes, the PSB also promoted the moso bamboo growth by increasing soil mineral N, AK and bamboo chlorophyll contents and stimulating functional microorganisms. Our study could provide a theoretical basis to improve soil nutrient utilization for moso bamboo with the PSB inoculations.

Changes of nitrogen and phosphorus removal pattern caused by alternating aerobic/anoxia from the perspective of microbial characteristics.

The purpose of this study was to compare the impact of different numbers of alternating aerobic/anoxic (A/O) cycles on pollutant removal. Three sequential batch reactors (SBRs) with varying numbers of alternating A/O cycles were established. Under the tertiary anoxic operating conditions, the removal efficiencies of chemical oxygen demand (COD), ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) were 88.73%, 89.56%, 72.15%, and 77.61%, respectively. Besides, alternating A/O affected the dominant microbial community relative abundance (Proteobacteria and Bacteroidetes) and increased microbial richness and diversity. It also increased the relative abundance of aerobic denitrifying, heterotrophic nitrifying, and denitrifying phosphorus removal bacteria to change N and P removal patterns. Furthermore, the abundance of carbohydrate metabolism and amino acid metabolism was improved by alternating A/O to improve organic matter and TN removal.

Bioengineering remediation of former industrial sites contaminated with chemical mixtures

Former gasworks sites are known to be contaminated with complex chemical mixtures that require remediation before redevelopment. Bioamendments such as biochar and spent mushroom compost (SMC) offer a green and sustainable remediation approach to help tackle this issue. However, the effectiveness of different biochar types and their interactions with the soil microbial community is still not well understood. To address this, a full factorial microcosm experiment was carried out using biochar derived from rice husk (RHB) and wheat straw (WSB) mixed with soil from a former gasworks site at varying concentrations (0%, 2.5%, and 5%), with and without SMC. The experiment aimed to evaluate the fate of contaminants including alkanes, PAHs, and metals, and their effect on the soil microbial community, as well as the implications for remediation endpoints. The results showed that the bioamendments had an average TPH reduction of 92%, with SMC and WSB-SMC having the highest degradation rates at 93%. While the bioamendments did not significantly affect the extent of TPH removal compared to the control, they did improve the degradation of high molecular weight (HMW) PAHs, particularly in RHB-SMC for EC17-20 (60%) and EC21-35 (62%) of total PAH concentration, and in WSB-SMC for HMW bioavailable PAH concentration (89%). The bioamendments also affected the partitioning and distribution of metals after 120 days of treatment, leading to decreased available phase fractions. The treatments increased microbial abundance in the soil, with Gram positives, Gram negatives, and fungi increasing by 4%, 8%, and 38%, respectively, after 120 days, particularly in SMC and mixed treatments. This was mirrored in increased microbial soil respiration. After 120 days, low metal (178 ± 5 mg/kg) and TPH (21 ± 7 mg/kg) bioavailability translated into higher EC50 (10624 ± 710 mg/L), indicating lower toxicity. There was a strong correlation between bioavailability and toxicity of TPH and metals with microbial relative abundance and activity. In summary, while green and sustainable remediation may accelerate the remediation process, monitored natural attenuation may be sufficient for site reclamation. However, this strategy, as demonstrated here, can reduce metal bioavailability, and promote the biodegradation of HMW PAHs.

Nonlinear Effects Induced by Interactions among Functional Groups of Bacteria and Fungi Regulate the Priming Effect in Malagasy Soils.

The priming effect (PE) occurs when fresh organic matter (FOM) supplied to soil alters the rate of decomposition of older soil organic matter (SOM). The PE can be generated by different mechanisms driven by interactions between microorganisms with different live strategies and decomposition abilities. Among those, stoichiometric decomposition results from FOM decomposition, which induces the decomposition of SOM by the release of exoenzymes by FOM-decomposers. Nutrient mining results from the co-metabolism of energy-rich FOM with nutrient-rich SOM by SOM-decomposers. While existing statistical approaches enable measurement of the effect of community composition (linear effect) on the PE, the effect of interactions among co-occurring populations (non-linear effect) is more difficult to grasp. We compare a non-linear, clustering approach with a strictly linear approach to separately and comprehensively capture all linear and non-linear effects induced by soil microbial populations on the PE and to identify the species involved. We used an already published data set, acquired from two climatic transects of Madagascar Highlands, in which the high-throughput sequencing of soil samples was applied parallel to the analysis of the potential capacity of microbial communities to generate PE following a 13C-labeled wheat straw input. The linear and clustering approaches highlight two different aspects of the effects of microbial biodiversity on SOM decomposition. The comparison of the results enabled identification of bacterial and fungal families, and combinations of families, inducing either a linear, a non-linear, or no effect on PE after incubation. Bacterial families mainly favoured a PE proportional to their relative abundances in soil (linear effect). Inversely, fungal families induced strong non-linear effects resulting from interactions among them and with bacteria. Our findings suggest that bacteria support stoichiometric decomposition in the first days of incubation, while fungi support mainly the nutrient mining of soil's organic matter several weeks after the beginning of incubation. Used together, the clustering and linear approaches therefore enable the estimation of the relative importance of linear effects related to microbial relative abundances, and non-linear effects related to interactions among microbial populations on soil properties. Both approaches also enable the identification of key microbial families that mainly regulate soil properties.

Succession and environmental response of sediment bacterial communities in the Liao River Estuary at the centenary scale

Microbial community succession in turbulent estuarine environments is key to the understanding of microbial community development in estuaries. Centennial-scale sediment core samples collected from the Liao River Estuary (LRE) channel bar and side beaches were studied for geochemistry and 16S rRNA gene-based bacterial analyses. The results showed that bacterial community composition significantly differed between the sediments of the two sides of the channel bar, with Campilobacterota and Bacteroidota being dominant bacterial phyla in the tributary (T1, T2) and mainstream (MS1, MS2) sediment, respectively. Co-occurrence network of the bacterial community at the genus level showed more centralized and compacted topological features in tributary with weaker hydrodynamic, and the keystone taxas were Halioglobus, Luteolibacter, and Lutibacter in the bacterial community. The bacterial network structure had more edges and larger average degree in LRE sediments from the stage of the year 2016–2009 and the stage before 1939, which was possibly related to hydrodynamic conditions and nutrients. Stochastic processes (dispersal limitation) were the key factors driving bacterial community assembly in the LRE sediments. In addition, total organic carbon (TOC), total sulfur (TS), and grain size were the main deterministic factors affecting the change of bacterial community structure. Relative microbial abundance has the potential to indicate geologically historical environmental changes. This study provided a new perspective to reveal the succession and response of bacterial communities under frequent fluctuation environments.

Gut Microbiota and Serum Metabolites in Individuals with Class III Obesity Without Type 2 Diabetes Mellitus: Pilot Analysis.

Background: Gut microbial composition seems to change in association with prediabetes. The purpose of this prospective cross-sectional study was to compare the composition of gut microbiota and energy metabolites between individuals with class III obesity but without type 2 diabetes mellitus (OB) and healthy normal weight controls. Methods: The subjects of this prospective cross-sectional study were participants recruited from a previous clinical trial (No: NCT02325804), with intervention focused on weight loss. We recruited 19 OB [mean age ± standard deviation (SD) was 35.4 ± 7.0 years, mean body mass index (BMI) ± SD was 48.8 ± 6.7 kg/m2] and 23 controls (mean age ± SD was 31.7 ± 14.8 years, mean BMI ± SD was 22.2 ± 1.7 kg/m2). Their fecal microbiota was categorized using specific primers targeting the V1-V3 region of 16S rDNA, whereas serum metabolites were characterized by nuclear magnetic resonance spectroscopy. Multivariate statistical analysis and Random Forest models were applied to discriminate predictors with the highest variable importance. Results: We observed a significantly lower microbial α-diversity (P = 0.001) and relative abundance of beneficial bacterium Akkermansia (P = 0.001) and the short-chain fatty acid-producing bacteria Eubacterium hallii (P = 0.019), Butyrivibrio (P = 0.024), Marvinbryantia (P = 0.010), and Coprococcus (P = 0.050) and a higher abundance of the pathogenic bacteria Bilophila (P = 0.018) and Fusobacterium (P = 0.022) in OB compared with controls. Notably, the Random Forest machine learning analysis identified energy metabolites (citrate and acetate), HOMA-IR, and insulin as important predictors capable of discriminating between OB and controls. Conclusions: Our results suggest that changes in gut microbiota and in serum acetate and citrate are additional promising biomarkers before progression to Type 2 diabetes. The non-invasive manipulation of gut microbiota composition in OB through a healthy lifestyle, thus, offers a new approach for managing class III obesity and associated disorders. ClinicalTrials.gov identifier: NCT02325804.

Positive effects of Cordyceps cateniannulata colonization in tobacco: Growth promotion and resistance to abiotic stress.

Entomopathogenic fungi can live in insects to cause disease and death and are the largest group of entomopathogenic microorganisms. Therefore, these fungi are best known for their microbial control potential. Importantly, they also have other beneficial effects, including promoting plant growth and development by colonizing plant. Here, the study sought to identify specific strains of the entomopathogenic fungus, Cordyceps cateniannulata that would form endophytic associations with tobacco, thus benefiting plant growth and resistance to abiotic stresses, thereby highlighting the application of entomopathogenic fungi in tobacco. The C. cateniannulata-tobacco symbiont was constructed by root irrigation. The effects of C. cateniannulata on tobacco growth were evaluated by measuring the maximum leaf length, maximum leaf width, number of leaves, plant height, stem thickness, stem circumference, dry and fresh shoot weight 7, 14, 21, and 28 days after colonization. The peroxidase, catalase, superoxide dismutase, and malondialdehyde were measured to observe the impact of C. cateniannulata on tobacco defense enzyme activity. Finally, high-throughput sequencing was used to access microbial communities in the rhizosphere, with data subsequently linked to growth indicators. After tobacco was inoculated with C. cateniannulata X8, which significantly promoted growth and related enzyme activity, malondialdehyde was decreased. The most significant impact was on peroxidase, with its activity being upregulated by 98.20, 154.42, 180.65, and 170.38% in the four time periods, respectively. The high throughput sequencing results indicated that C. cateniannulata had changed the rhizosphere microbial relative abundances, such as increasing Acidobacteria and Ascomycetes, and decreasing Actinomycetes and Basidiomycetes. The redundancy analysis showed that C. cateniannulata significantly boosted tobacco growth by reducing the abundance of specific dominant genera such as Stachybotrys, Cephalotrichum, Streptomyces, Isoptericola, and Microbacterium. Specific strains of C. cateniannulata can be introduced into host plants as endophytes, resulting in promotion of host plant growth and increased resistance to abiotic stress and microbial pathogens. The study provides a foundation for future studies of C. cateniannulata as an ecological agent.

Different microbial genera drive methane emissions in beef cattle fed with two extreme diets.

The ratio of forage to concentrate in cattle feeding has a major influence on the composition of the microbiota in the rumen and on the mass of methane produced. Using methane measurements and microbiota data from 26 cattle we aimed to investigate the relationships between microbial relative abundances and methane emissions, and identify potential biomarkers, in animals fed two extreme diets - a poor quality fresh cut grass diet (GRASS) or a high concentrate total mixed ration (TMR). Direct comparisons of the effects of such extreme diets on the composition of rumen microbiota have rarely been studied. Data were analyzed considering their multivariate and compositional nature. Diet had a relevant effect on methane yield of +10.6 g of methane/kg of dry matter intake for GRASS with respect to TMR, and on the centered log-ratio transformed abundance of 22 microbial genera. When predicting methane yield based on the abundance of 28 and 25 selected microbial genera in GRASS and TMR, respectively, we achieved cross-validation prediction accuracies of 66.5 ± 9% and 85 ± 8%. Only the abundance of Fibrobacter had a consistent negative association with methane yield in both diets, whereas most microbial genera were associated with methane yield in only one of the two diets. This study highlights the stark contrast in the microbiota controlling methane yield between animals fed a high concentrate diet, such as that found on intensive finishing units, and a low-quality grass forage that is often found in extensive grazing systems. This contrast must be taken into consideration when developing strategies to reduce methane emissions by manipulation of the rumen microbial composition.

Abstract 3797: Fecal miRNA profiles and gut metagenome composition in Lynch syndrome: results from a mouse model study and human subjects

Abstract Bsacground: Lynch Syndrome (LS) is an inherited cancer syndrome associated with an increased lifetime risk of colorectal cancer (CRC) and characterised by germline mutations in DNA mismatch repair (MMR) genes. Abnormalities in the function of MMR genes lead to errors during DNA replication, including microsatellite instability. Despite regular colonoscopies, up to 15% of LS patients still develop CRC. Gut microbiome, bowel inflammation, the environment and host genetic and epigenetic factors are involved in CRC development. In this sense, the concomitant analysis of stool host microRNA (miRNA) profiles and gut microbiome composition may arise to the identification of specific fecal markers in LS explaining the molecular basis for the development of cancer in these patients. PURPOSE: In the present study, the fecal miRNome and microbiome were characterized in a time progression in an in vivo model using a mismatch repair deficient mice model that recapitulates human LS. The main aim was to evaluate the changes and crosstalk of miRNAs released in the stool by the host and the microbial population residing in the gut during the carcinogenesis process induced in animals. Findings in mice were compared and correlated to data obtained from a cohort of human subjects affected by LS. Methods: We used an in vivo model for LS based on a conditional knockout mouse with the tissue-specific inactivation of Msh2 (Msh2LoxP) in the intestinal mucosa, combining Msh2LoxP allele with the Villin-Cre transgene (VCMsh2LoxP). Stool from mice were collected at different time points (6, 9 and 12 months of age). Small RNA-sequencing (sRNA-seq) and shotgun metagenomics analyses were performed in stool from all samples. In concomitance, we collected 78 stool samples of clinically diagnosed LS subjects, at different follow up time. At the sampling, 36 resulted negative for colorectal adenomas/lesions, 12 were negative but with a previous history of lesions, 23 presented a neoplasia and 6 developed a lesion in the follow-up. Twenty-two stool samples from healthy subjects were used as controls. Results: In mice, preliminary results from sRNA-seq and metagenomics analyses showed several dysregulated miRNAs and differential microbial relative abundances, either between VCMsh2loxP and controls or at different time points. In humans, we identified 41 and 17 miRNAs respectively up- and downregulated in LS subjects who presented a lesion compared to those not having any lesion at follow-up. In the same comparison the metagenomic data showed significantly different microbial abundances, including those of Eubacterium ramulus. Conclusions: This is the first study characterizing the concomitant alterations in microbial composition and host miRNome overtime in relation to the onset of cancerous/precancerous lesions due to LS. Citation Format: Giulia Francescato, Giulio Ferrero, Marc Beltrà, Sonia Tarallo, Giulia Piaggeschi, Carla Di Battista, Antonio Francavilla, Carlijn Bruggeling, Fabio Penna, Barbara Pardini, Paola Costelli, Annemarie Boleij, Alessio Naccarati. Fecal miRNA profiles and gut metagenome composition in Lynch syndrome: results from a mouse model study and human subjects. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3797.

Taxonomical and functional responses of microbial communities from forest soils of differing tree species diversity to drying-rewetting cycles

The predicted increases in drought in many forest ecosystems may alter soil microbial community diversity and activity, which may further depend on tree species richness. Shifts in microbial community composition and activity could engender changes in ecosystem function, notably, in soil greenhouse gas emissions and C storage. Using soils from mono-specific and mixed three-species forest stands from across Europe, we performed a microcosm experiment to test how soil microbial taxonomic and catabolic diversity are affected by repeated drying-rewetting (DRW) cycles and tree species mixing. We used Illumina sequencing and MicroResp™ analyses to explore community-level changes between microbial functional groups. DRW decreased bacterial richness and carbon substrate use diversity and increased fungal Shannon diversity. Additionally, microbial communities exposed to DRW changed their consumption of 11 out of 15 substrates significantly, suggesting microbial functional shifts. The legacy effect of tree species mixing influenced the structure of the microbial communities (i.e. taxonomic differential abundance) although, community weighted mean (CWM) values of absorptive root traits appeared to affect more strongly microbial richness, relative abundance, and Shannon diversity. No significant tree species mixing:DRW interaction was found for most microbial variables, except for the use of certain substrates and potentially differential abundance. Our data from a laboratory experiment with soils from different forest ecosystems underline that drought may cause shifts in microbial taxonomic and catabolic diversity, while tree species influences primarily taxonomic diversity through root traits.

Dynamics and diversity of symbiotic bacteria in Apolygus lucorum at different developmental stages

BackgroundApolygus lucorum is a worldwide omnivorous pest damaging a range of crops and causing great economic losses. Symbiotic bacteria living in insects play a key role in the nutrition, physiology, and behavior of hosts. Here, we present an experiment using Illumina HiSeq sequencing targeting the V3–V4 regions of bacteria’s 16S rRNA throughout the entire life cycle of A. lucorum.ResultsThe first and second instar nymphs have the largest alpha diversity compared with other life stages of the insect. Bacterial phyla Proteobacteria (72.29%), Firmicutes (15.24%), Actinobacteria (7.76%) exhibit the largest relative abundance in all developmental stages. Erwinia (23.97%) and Lactococcus (10.62%) are the two genera with the highest relative abundance. The relative abundance of Erwinia in the nymph stage is significantly greater than the adult stage, and the relative abundance of Lactococcus in 6-day-old and 9-day-old adult females is higher compared with adult males.ConclusionsThese results reveal that microbial community composition and relative abundance shift dynamically at different life stages, implying that different bacterial phyla and genera may have specific roles in specific life stages such as metabolism, nutrition absorption, detoxification, and reproduction. This study reveals for the first time the community composition and ecological dynamics of symbiotic bacteria throughout the life stages of A. lucorum, and thus may provide insight to new strategies for pest control.

Analysis of Microbial Communities in Membrane Biofilm Reactors Using a High-Density Microarray

Membrane biofilm reactors (MBfRs) have attracted more and more attention in the field of wastewater treatment due to their advantages of high mass transfer efficiency and low-carbon emissions. There are many factors affecting their nitrogen removal abilities, such as operation time, electron donor types, and operation modes. The operation time is directly related to the growth status of microorganisms, so it is very important to understand the effect of different operation times on microbial composition and community succession. In this study, two parallel H2-based MBfRs were operated, and differences in microbial composition, community succession, and NO3--N removal efficiency were investigated on the 30th day and the 60th day of operation. The nitrogen removal efficiency of MBfRs with an operation time of 60 days was higher than that of MBfRs with an operation time of 30 days. Proteobacteria was the dominant phylum in both MBfRs; however, the composition of the microbial community was quite different. At the class level, the community composition of Proteobacteria was similar between the two MBfRs. Alphaproteobacteria was the dominant class in MBfR, and Betaproteobacteria and Gammaproteobacteria were also in high proportion. Combined with the analysis of microbial relative abundance and concentration, the similarity of microbial distribution in the MBfRs was very low on day 30 and day 60, and the phylogenetic relationships of the top 50 dominant universal bacteria and Proteobacteria were different. Although the microbial concentration decreased with the extension of the operation time, the microbial abundance and diversity of specific functional microorganisms increased further. Therefore, the operation time had a significant effect on microbial composition and community succession.

Nanopore sequencing of DNA barcodes to unveil the diversity of fungal mock communities

Background: The fungal component of the gut microbiome has been underrepresented in most gut microbiome studies. While next-generation sequencing (NGS) approaches have been used to assess the diversity and role of the gut mycobiome, differences in experimental design and downstream analyses may induce bias and differential outcomes. This study assessed the capacity of nanopore sequencing to retrieve the microbial profile and relative abundance of a mock fungal community comprised of Candida glabrata, Meyerozyma guilliermondii, Pichia kudriavzevii, Clavispora lusitaniae and Candida parapsilosis. Methods: The approach was implemented using the MinION system and involved the analysis of sequencing libraries made from equimolar mixtures of the PCR-amplified internal transcriber spacer genomic regions of the target species. Results: Nanopore sequencing successfully retrieved the composition of the fungal mock community in terms of the different taxa present. However, the approach was unable to correctly assess the expected relative abundances of each species in the same community, showing some yet undetermined bias that may be related to the size of the respective target DNA fragments. Clavispora lusitaniae was consistently overrepresented in the mixtures, while C. glabrata was underrepresented. The remaining three species showed relative abundances more aligned with the expected values of an equimolar mixture. Conclusions: Although not yielding the expected results for the relative abundances, the values obtained from independent sequencing runs were similar for all species, suggesting a good reliability but questionable accuracy in this sequencing approach.

Analysis of Bacterial Diversity in Fermented Grains of Baijiu Based on Culturomics and Amplicon Sequencing

Baijiu is a traditional distilled liquor in China. The unique flavor developed during the fermentation process of Baijiu is closely related to the microorganisms in the fermented grains of the Baijiu. Fermented grain is a solid material that has not been distilled after the fermentation of Baijiu. It is of great significance to study the bacterial diversity in fermented grains and to isolate and culture them to reveal the formation mechanism of the flavor substances in Baijiu. In this study, the diversity of bacteria in fermented grains was studied by the combination of amplicon sequencing and culturomics, and a pure culture of culturable strains was obtained. The results of amplicon sequencing showed that the bacteria detected in the fermented grains were classified into 5 phyla, 8 classes, 24 orders, 34 families, and 45 genera, of which Lactobacillus (66.95%) and Acetobacter (32.36%) were the dominant genera. By using the method of culturomics, five pH gradients (pH = 3, 4, 5, 6, and 7) of enrichment culture medium and solid medium with different components were designed to enrich and isolate the culturable bacteria in the fermented grains. A total of 323 strains of bacteria were obtained, belonging to 53 genera and 118 species, and 14 suspected new species were obtained. Among the bacteria isolated by the culturomics, 14 genera were detected by amplicon sequencing, and 39 genera were not detected, indicating that the culturomics method can isolate and culture bacteria with low abundance in fermented grains. Compared with the traditional culture method, culturomics expanded the culturable bacteria in the fermented grains to 188%. The diversity of the bacteria in the fermented grains of Baijiu was analyzed by amplicon sequencing and culturomics, and the microbial community composition and relative abundance of fermented grains were comprehensively revealed. At the same time, the acquisition of more pure cultures of culturable bacteria provides more choices for the liquor-making microbial resource library.

Abstract P425: Diets Enriched in Stearate, Palmitate, and Oleate Differentially Modulate Gut Microbiome Composition in Post-Menopausal Women

Objective: Dietary stearic acid (18:0), a major saturated fatty acid (SFA) in Western diets, does not raise plasma LDL-C concentrations relative to other shorter chain SFAs (palmitic [16:0], myristic [14:0] and lauric [12:0]), and is associated with lower CVD risk. We investigated whether the cardioprotective effects of 18:0 and its metabolic product oleic acid (18:1, a monounsaturated fatty acid) relative to 16:0 is mediated via alterations in the gut microbiome. Methods: Twenty mildly hypercholesterolemic (LDL-C>100mg/dL) post-menopausal women (50-85 years; BMI 25-35kg/m 2 ) consumed each of 3 isocaloric diets for 5 weeks according to a randomized controlled cross-over design. Diets provided 55%E carbohydrate, 15%E protein and 30%E fat with half of the fat provided by 16:0, 18:0 or 18:1, respectively. Fecal samples were collected at the end of each diet phase and shotgun metagenomic sequencing was performed. Alpha diversity (Shannon index, Simpson index and observed counts) was compared between diet groups using two-sample non-parametric tests. Beta-diversity was assessed using Bray-Curtis dissimilarity with PERMANOVA test. Differences in metagenomic features by diet group were evaluated using Partial Least Squares-Discriminant Analysis (PLS-DA) models of pairwise diet differences developed using the R package ‘mixOmics’. Results: No significant differences were observed in alpha and beta diversity between diet groups. However, the variability in microbial relative abundance was greater after participants consumed the 18:0 and 18:1 diets compared to the 16:0 diet. Specifically, mean relative abundance of Bacterioides dorei , Bacteroides vulgatus , and Ruminococcus were highest after participants consumed the 18:0 relative to the 16:0 diet and intermediate after the 18:1 diet. The relative abundance of Coprococcus , Parabacteroides distasonis , Coprobacillus and Blautia were higher after participants consumed the 18:1 relative to the 16:0 diet. These microbial species have been associated with several anti-inflammatory pathways and decreased bacterial lipopolysaccharide production. Conclusion: These data document modest but distinctive effects of dietary SFAs on gut microbiome composition and functionality, suggesting that the favorable effects of 18:0 and 18:1 relative to 16:0 on CVD risk factors could be mediated, in part, by the gut microbiome.

Current evidence and clinical relevance of drug-microbiota interactions in inflammatory bowel disease.

Inflammatory bowel disease (IBD) is a chronic relapsing-remitting disease. An adverse immune reaction toward the intestinal microbiota is involved in the pathophysiology and microbial perturbations are associated with IBD in general and with flares specifically. Although medical drugs are the cornerstone of current treatment, responses vary widely between patients and drugs. The intestinal microbiota can metabolize medical drugs, which may influence IBD drug (non-)response and side effects. Conversely, several drugs can impact the intestinal microbiota and thereby host effects. This review provides a comprehensive overview of current evidence on bidirectional interactions between the microbiota and relevant IBD drugs (pharmacomicrobiomics). Electronic literature searches were conducted in PubMed, Web of Science and Cochrane databases to identify relevant publications. Studies reporting on microbiota composition and/or drug metabolism were included. The intestinal microbiota can both enzymatically activate IBD pro-drugs (e.g., in case of thiopurines), but also inactivate certain drugs (e.g., mesalazine by acetylation via N-acetyltransferase 1 and infliximab via IgG-degrading enzymes). Aminosalicylates, corticosteroids, thiopurines, calcineurin inhibitors, anti-tumor necrosis factor biologicals and tofacitinib were all reported to alter the intestinal microbiota composition, including changes in microbial diversity and/or relative abundances of various microbial taxa. Various lines of evidence have shown the ability of the intestinal microbiota to interfere with IBD drugs and vice versa. These interactions can influence treatment response, but well-designed clinical studies and combined in vivo and ex vivo models are needed to achieve consistent findings and evaluate clinical relevance.

Dynamics of soil microbiome throughout the cultivation life cycle of morel (Morchella sextelata).

Although Morchella sextelata (morel) is a well-known, edible, and medicinal fungus widely cultivated in China, the dynamics and roles of its soil microbiome during cultivation are unclear. Using rhizosphere soil samples collected throughout the M. sextelata cultivation life cycle, we conducted a high-throughput metagenomic sequencing analysis, with an emphasis on variations in soil microbial composition, characteristic biomarkers, and ecological functions. We found that microbial relative abundance, alpha diversity, and structure varied significantly among fungal growth stages. A total of 47 stage-associated biomarkers were identified through a linear discriminant analysis of effect size. In addition, horizontal comparison of soil microbiomes exhibiting successful and failed primordium formation further confirmed primordium-associated microbes with possible key roles in primordium formation. A microbial function analysis revealed that nutrient metabolism-related pathways were enriched during mycelium and fruiting body stages, whereas the signal transduction pathway was enriched during the primordium stage. This result indicates that diverse microbes are required at different growth stages of M. sextelata. Our research has revealed the dynamic scenario of the soil microbiome throughout the cultivation life cycle of M. sextelata. The high-resolution microbial profiles uncovered in the present study provide novel insights that should contribute to the improvement of morel cultivation using microbial inoculants.