Microbial Community Profiles Research Articles

The impact of diets containing Hermetia illucens meal on the growth, intestinal health, and microbiota of gilthead seabream (Sparus aurata)

The present study investigated the effect of replacing fishmeal (FM) with insect meal of Hermetia illucens (HI) in the diet of Sparus aurata farmed inshore on growth, gut health, and microbiota composition. Two isolipidic (18% as fed) and isoproteic (42% as fed) diets were tested at the farm scale: a control diet without HI meal and an experimental diet with 11% HI meal replacing FM. At the end of the 25-week feeding trial, final body weight, specific growth rate, feed conversion rate, and hepatosomatic index were not affected by the diet. Gross morphology of the gastrointestinal tract and the liver was unchanged and showed no obvious signs of inflammation. High-throughput sequencing of 16S rRNA gene amplicons (MiSeq platform, Illumina) used to characterize the gut microbial community profile showed that Proteobacteria, Fusobacteria, and Firmicutes were the dominant phyla of the gut microbiota of gilthead seabream, regardless of diet. Dietary inclusion of HI meal altered the gut microbiota by significantly decreasing the abundance of Cetobacterium and increasing the relative abundance of the Oceanobacillus and Paenibacillus genera. Our results clearly indicate that the inclusion of HI meal as an alternative animal protein source positively affects the gut microbiota of seabream by increasing the abundance of beneficial genera, thereby improving gut health and maintaining growth performance of S. aurata from coastal farms.

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts.

It has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis. In this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus. The analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified. This study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained.

Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs

The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined the multitissue microbial biogeography of healthy Fischer 344 rats across their lifespan. Microbial community profiling data were extracted and integrated with host transcriptomic data from the Sequencing Quality Control consortium. Unsupervised machine learning, correlation, taxonomic diversity and abundance analyses were performed to determine and characterize the rat microbial biogeography and identify four intertissue microbial heterogeneity patterns (P1–P4). We found that the 11 body habitats harbored a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundance progressively declined in lungs from breastfed newborn to adolescence/adult, and was below detectable levels in elderly rats. Bioinformatics analyses indicate that the abundance of LAB may be modulated by the lung–immune axis. The presence and levels of LAB in lungs were further evaluated by PCR in two validation datasets. The lung, testes, thymus, kidney, adrenal and muscle niches were found to have age-dependent alterations in microbial abundance. The 357 microbial signatures were positively correlated with host genes in cell proliferation (P1), DNA damage repair (P2) and DNA transcription (P3). Our study established a link between the metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures could be useful for microbiome therapeutic approaches to human health and life quality enhancement.

Temporal profiling of sediment microbial communities in the Three Gorges Reservoir Area discovered time-dissimilarity patterns and multiple stable states

Microbial communities play vital roles in cycling nutrients and maintaining water quality in aquatic ecosystems. To better understand the dynamics of microbial communities and to pave way to effective ecological remediation, it's essential to reveal the temporal patterns of the communities and to identify their states. However, research exploring the dynamic changes of microbial communities needs a large amount of time-series data, which could be an extravagant requirement for a single study. In this research, we overcame this challenge by conducting a meta-analysis of years of accumulations of 16S rRNA high-throughput sequencing data from the Three Gorges Reservoir Area (TGRA), an ecological and environmental hotspot. For better understanding the microbial communities time-dissimilarity dynamics, three microbial communities time-dissimilarity patterns were hypothesized, and the linear pattern in the TGRA was validated. In addition, to explore the stability of microbial communities in the TGRA, two alternative stable states were revealed, and their differences in community richness, alpha diversity indices, community composition, ecological network topological properties, and metabolic functions were demonstrated. In short, two states of microbial communities showed distinct richness and alpha diversity indices, and the communities in one state were more dominated by Halomonas and Nitrosopumilaceae genera, facilitating nitrogen cycling metabolic processes; whilst the main genera of the other state were Bathyarchaeia and Methanosaeta, which favored methane-related metabolism. Moreover, different studies and environmental differences between mainstream and tributaries were attributed as the potential inducing factors of the state division. Our study provides a comprehensive insight into the dynamics and stability of microbial communities in the TGRA, and a reference for future studies on microbial community dynamics.

Microbial diversity and prediction function profiling of microbial communities in rose jam

AbstractThe microbial diversity of rose jam was analyzed by high‐throughput sequencing, along with functional prediction of the bacterial community. The results indicate that Pseudomonas, Pantoea, and Burkholderia emerged were the top three dominant bacterial groups. Proteobacteria was particularly abundant in R4 (99.1%) and R6 (96.12%). Zygosaccharomyces, unclassified fungi, and Botrytis constituted the top three fungal groups. The presence of unclassified OTUs was observed in all samples, particularly in R6 (52.36%), R8 (45.28), and R9 samples (39.57%). Gene prediction using PICRUSt revealed the existence of multiple KEGG functional modules associated with human metabolism in each rose jam sample. The presence of a high abundance of functional genes indicated the microbial community's diverse wide range of microgenetic resources that can be further explored for research purposes. The microbial community found in rose jam exhibits remarkable diversity and encompasses valuable functional information relevant to human health.

An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform.

Recent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms. We have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run. The unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits.

Pyrosequencing analysis of bacterial community changes in dental unit waterlines after chlorogenic acid treatment.

The contamination of dental unit waterlines (DUWLs) poses a significant risk of cross-infection in dentistry. Although chemical disinfectants have been effective in reducing number of bacteria, they do have limitations. This study aimed to investigate the potential of chlorogenic acid, a natural substance with broadspectrum antibacterial properties, for treating DUWLs. Over a period of three months, we analyzed the microbial communities in 149 DUWLs samples collected from 5 dental units using high-throughput pyrophosphate sequencing. The results revealed that chlorogenic acid treatment had a significant impact on the microbial community profile in the DUWLs, with the most significant changes occurring within the first 15 days and stabilization observed in the last 30 days. The predominant genera detected in the samples were Bacteroides, Lactobacillus, Streptococcus, Methylobacterium, and Phreatobacter. Additionally, the relative abundance of certain beneficial bacteria, such as Alloprevotella, Roseburia, and Blautia, increased, while the presence of opportunistic pathogens like Mycobacteria significantly decreased. The functional prediction analysis using the KEGG database indicated a decrease in the pathogenicity of the bacterial community in the DUWLs following chlorogenic acid treatment. This study introduces a novel approach for the prevention and treatment of infections associated with dental care.

Alterations in the composition and metabolite profiles of the saline-alkali soil microbial community through biochar application

Saline-alkali soil poses significant chanllenges to sustainable development of agriculture. Although biochar is commonly used as a soil organic amendment, its microbial remediation mechanism on saline-alkali soil requires further confirmation. To address this, we conducted a pot experiment using cotton seedlings to explore the potential remediation mechanism of rice straw biochar (BC) at three different levels on saline-alkaline soil. The results showed that adding of 2% biochar greatly improved the quality of saline-alkaline soil by reducing pH levels, electrical conductivity (EC), and water-soluble ions. Moreover, biochar increased the soil organic matter (SOM), nutrient availability and extracellular enzyme activity. Interestingly, it also reduced soil salinity and salt content in various cotton plant tissues. Additionally, biochar had a notable impact on the composition of the microbial community, causing changes in soil metabolic pathways. Notably, the addition of biochar promoted the growth and metabolism of dominant salt-tolerant bacteria, such as Proteobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota. By enhancing the positive correlation between microorganisms and metabolites, biochar alleviated the inhibitory effect of salt ions on microorganisms. In conclusion, the incorporation of biochar significantly improves the soil microenvironment, reduces soil salinity, and shows promise in ameliorating saline-alkaline soil conditions.

Semen microbiota are dramatically altered in men with abnormal sperm parameters

There has recently been an explosion of studies implicating the human microbiome in playing a critical role in many disease and wellness states. The etiology of abnormal semen analysis (SA) parameters is not identified in 30% of cases; investigations involving the semen microbiome may bridge this gap. Here, we explore the relationship between the semen microbiome and alterations of sperm parameters. We recruited men presenting for fertility evaluation or vasectomy consultation with proven biological paternity. SA and next generation sequencing was performed. Differential abundance testing using Analysis of composition of Microbiota with Bias Correction (ANCOM-BC) was performed along with canonical correlational analysis for microbial community profiling. Men with abnormal (N = 27) sperm motility showed a higher abundance of Lactobacillus iners compared to those with normal (N = 46) sperm motility (mean proportion 9.4% versus 2.6%, p = 0.046). This relationship persisted on canonical correlational analysis (r = 0.392, p = 0.011). Men with abnormal sperm concentration (N = 20) showed a higher abundance of Pseudomonas stutzeri (2.1% versus 1.0%, p = 0.024) and Pseudomonas fluorescens (0.9% versus 0.7%, p = 0.010), but a lower abundance of Pseudomonas putida (0.5% versus 0.8%, p = 0.020), compared to those with normal sperm concentration (N = 53). Major limitations are related to study design (cross-sectional, observational). Our results suggest that a small group of microorganisms may play a critical role in observed perturbations of SA parameters. Some of these microbes, most notably Lactobacillus iners, have been described extensively within other, fertility-related, contexts, whereas for others, this is the first report where they have potentially been implicated. Advances in our understanding of the semen microbiome may contribute to potentially new therapeutic avenues for correcting impairments in sperm parameters and improving male fertility.

Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples.

Combining multiple displacement amplification (MDA) with metagenomics enables the analysis of samples with extremely low DNA concentrations, making them suitable for high-throughput sequencing. Although amplification bias and nonspecific amplification have been reported from MDA-amplified samples, the impact of MDA on metagenomic datasets is not well understood. We compared three MDA methods (i.e. bulk MDA, emulsion MDA, and primase MDA) for metagenomic analysis of two DNA template concentrations (approx. 1 and 100pg) derived from a microbial community standard "mock community" and two low biomass environmental samples (i.e. borehole fluid and groundwater). We assessed the impact of MDA on metagenome-based community composition, assembly quality, functional profiles, and binning. We found amplification bias against high GC content genomes but relatively low nonspecific amplification such as chimeras, artifacts, or contamination for all MDA methods. We observed MDA-associated representational bias for microbial community profiles, especially for low-input DNA and with the primase MDA method. Nevertheless, similar taxa were represented in MDA-amplified libraries to those of unamplified samples. The MDA libraries were highly fragmented, but similar functional profiles to the unamplified libraries were obtained for bulk MDA and emulsion MDA at higher DNA input and across these MDA libraries for the groundwater sample. Medium to low-quality bins were possible for the high input bulk MDA metagenomes for the most simple microbial communities, borehole fluid, and mock community. Although MDA-based amplification should be avoided, it can still reveal meaningful taxonomic and functional information from samples with extremely low DNA concentration where direct metagenomics is otherwise impossible.

Test of two membrane filter types for biomass collectionin community profiling by metabarcoding

With the rapid development of microorganism biodiversity estimation and community profiling via DNA metabarcoding, there is a growing need to identify key stages affecting the results of experiment. In order to ensure high-quality reproducible results, all potential sources of bias should be explored. While bioinformatic pipelines can be often corrected and optimized to recalculate results, the initial steps of sample collection procedure, potentially influencing the downstream results of bacterial community profiling, are much harder to correct easily, without repeating the whole experiment. We examined the differences of the amplicon bacterial community profiles generated from aquatic microbial communities captured by polycarbonate (PC) and cellulose acetate (CA) filters. The microbial community profiles were shown to be significantly different by biodiversity. When using a PC-filters, alpha- and beta-diversity of communities were significantly higher. Differential abundance analysis showed enrichment of major cyanobacterial OTUs in CA-treated communities. Based on these results, the use of PC-filters is the most optimal for bacterial community profiling by metabarcoding of the 16S rRNA gene fragments.

Dynamic changes in the gel properties, microbial community, and volatile flavor profile of Spanish mackerel (Scomberomorus niphonius) sausages inoculated with Lactiplantibacillus plantarum CY1-2.

Spanish mackerel is an important economic fish species in China, but corruption undermines its overall economic value. Fermentation serves as a crucial technique for preserving perishable fish in developing countries. This study aimed to examine the dynamic changes in the gel properties, physicochemical properties, microbial diversity, and volatile flavor compounds (VFCs) of Spanish mackerel sausages inoculated with Lactiplantibacillus plantarum CY1-2 during fermentation. The correlation between key microorganisms and VFCs was explored using a two-way orthogonal partial least squares analysis. The results showed that the group inoculated with strain CY1-2 exhibited significant improvements compared with the control group after 40 h of fermentation. Specifically, gel strength increased by 207.7%, total free amino acids increased by 37.49%, DPPH and ABTS radical scavenging rates increased by 34.12% and 58.73%, and TVB-N levels decreased by 54.2%, respectively. In addition, using gas chromatography-mass spectrometry, 36 VFCs were detected in fermented sausages, including 9 aldehydes, 9 hydrocarbons, 7 alcohols, 4 acids, 2 ketones, and 5 esters. High-throughput sequencing demonstrated that the bacterial profiles were altered in sausages inoculated with strain CY1-2 during fermentation. Enhydrobacter dominated initially but was quickly replaced by Macrococcus after 8 h of fermentation, while Lactobacillus became the dominant genus after 40 h. Correlation analysis revealed that Lactobacillus and Staphylococcus played important roles in the production of VFCs in the fermented sausages. Notably, Lactobacillus was positively associated with 2-undecanone, pentadecane, and hexanal. This study confirmed that strain CY1-2 inoculation could enable the production of high-quality fermented fish sausages.

Toward functional profiling for eDNA‐based monitoring in coastal environments: A comparison of three approaches

AbstractCoastal environments, crucial and intricate ecosystems, face threats from human activities like pollution, eutrophication, and climate change. Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics. Results revealed significant functional diversity across all sampling sites, irrespective of their environmental status. Most predicted KEGG Orthologs (KOs) showed consistency between metagenomics and Tax4Fun datasets, with correlated abundances. However, abundances derived from GeoChip did not correlate with either dataset. When comparing estuaries based on environmental status, Tax4Fun and metagenomics identified over 24% of KOs with significantly different abundances. KOs overrepresented in estuaries with a poor ecological status displayed an abundance of pathways associated with anaerobic metabolism, such as methanogenesis.

Anode biomass rather than soluble organic matter is fuel for electricity production in microbial fuel cell at longer hydraulic retention time

This study presents a novel method for independently calculating organic matter (OM) removal and electricity generation in a microbial fuel cell (MFC) treating sewage. This methodology used OM concentration as the exclusive variable for input, facilitating the prediction of electricity generation with variable Coulombic efficiency. The employed MFC, of tubular design, incorporates an air core surrounded by a carbon-based cathode, an anion exchange membrane, nonwoven graphite fabric, and encircled by twelve carbon brush anodes. This setup successfully reduced chemical oxygen demand (COD) from 180 to 50 mg L−1 and biological oxygen demand (BOD) from 84 to 15 mg L−1 within a 35 h hydraulic retention time (HRT). The resulting effluent BOD satisfies Japanese wastewater treatment standards. In the early HRT phase, the MFC exhibited rapid OM reduction, followed by a stabilization of OM concentration. Despite varying HRTs and the sustained OM levels at prolonged HRTs, the MFC consistently generated 0.29 ± 0.14 A m−2. This apparent contradiction prompted the consideration of additional OM sources from the anode biomass (Cb). Calculating electricity production based on OM concentration rather than OM degradation was achieved by assessing anode resistance (RAn) across different levels of OM supplementation, employing the Butler–Volmer equation. This approach, incorporating considerations for Cb and RAn, accurately reproduced MFC performance. It was observed that OM supplementation from Cb constituted 50% at 11 h HRT and escalated to 90% at 27 h HRT. Further analysis, including 16S rRNA gene-based microbial community profiling, indicated that higher cathode resistance (RCat) at 1.0 Ω m2, compared to a minimum RAn of 0.10 Ω m2, favored methanogenesis over electrogenesis on the carbon brushes. This finding underscores the importance of reducing RCat and minimizing electrode distance, coupled with enhancing the specific surface area of both electrodes, as crucial factors for the advancement of MFC technology.

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.

Microbiological impacts of acid mine drainage on urban agriculture in Soweto, South Africa

The late 17th century discovery of gold in Johannesburg was accompanied by skewed income distribution in the world's most unequal society and more prosaic curses like acid mine drainage (AMD). This acid water contaminates ecosystems such as patches of urban agriculture that communities rely on to supplement income and nutritional needs. We investigated the extent to which AMD contaminates streams, irrigation water and subsequently, soil and vegetation on small-scale farms. We targeted microbial communities as the first line of biotic casualties in AMD infiltrated substrates. Sites were all in Soweto, Johannesburg, the first was just adjacent to a mine dump, the second was in a midstream section and the last was downstream where locals cultivate fields. We tested contamination of river sediment, river water, cultivated and uncultivated soil, borehole water used for irrigation and the crops themselves. The Biolog EcoPlate™ microbial community profiling kit was used, it measures the ability of microbes to use various carbon sources. The MicrotoxⓇ bio-assay was also used, it exploits a luminescent bacterium to indicate the level of biological toxicity in a medium. Both methods suggest severe contamination of environmental substrates close to the AMD source. The contamination attenuates downstream but was detected in soil, water and crops ~20 km away from the mine. Therefore, the impacts of mining are systemic in the catchment and authorities must appreciate the seriousness of the situation so that mitigation strategies can devised and implemented immediately.

Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions.

While pressure is a significant characteristic of petroleum reservoirs, it is often overlooked in laboratory studies. To clarify the composition and metabolic properties of microbial communities under high-pressure conditions, we established methanogenic and sulfate-reducing enrichment cultures under high-pressure conditions using production water from the Jilin Oilfield in China. We utilized a metagenomics approach to analyze the microbial community after a 90-day incubation period. Under methanogenic conditions, Firmicutes, Deferribacteres, Ignavibacteriae, Thermotogae, and Nitrospirae, in association with the hydrogenotrophic methanogen Archaeoglobaceae and acetoclastic Methanosaeta, were highly represented. Genomes for Ca. Odinarchaeota and the hydrogen-dependent methylotrophic Ca. Methanosuratus were also recovered from the methanogenic culture. The sulfate-reducing community was dominated by Firmicutes, Thermotogae, Nitrospirae, Archaeoglobus, and several candidate taxa including Ca. Bipolaricaulota, Ca. Aminicenantes, and Candidate division WOR-3. These candidate taxa were key pantothenate producers for other community members. The study expands present knowledge of the metabolic roles of petroleum-degrading microbial communities under high-pressure conditions. Our results also indicate that microbial community interactions were shaped by syntrophic metabolism and the exchange of amino acids and cofactors among members. Furthermore, incubation under in situ pressure conditions has the potential to reveal the roles of microbial dark matter.

Dietary Qi-Weng-Huangbo powder enhances growth performance, diarrhoea and immune function of weaned piglets by modulating gut health and microbial profiles.

The evolution of nutritional strategies to improve the gut health and microbiota profiles of early-weaned piglets is essential to reduce diarrhoea caused by weaning stress. Therefore, the aim of this study was to determine the effects of dietary supplementation of Qi-Weng-Huangbo powder, a traditional herbal medicine consisting of a mixture of Pulsatilla chinensis, Chinese Schneid and Astragalus extracts (PCE), on the growth performance, diarrhoea rate, immune function and intestinal health of weaned piglets. 162 piglets were randomly assigned to the CON group (no PCE added), the PCEL group (300 mg/kg PCE) and the PCEH group (500 mg/kg PCE) at the end of the third week post farrowing. There were 9 replicates of each group with 6 pigs per replicate. The experiment lasted for 28 days and sampling was performed on the final day. The results showed that the PCE diet increased the average daily gain (ADG) and final body weight (BW) compared to the CON group. Both supplemented doses of PCE reduced the faecal scores of piglets, and the diarrhoea rate in the PCEL group was significantly lower than that in the CON group. The application of PCE diets promoted the development of the spleen in piglets and up-regulated serum immunoglobulin concentrations to enhance immune function, which was also reflected in the down-regulated gene expression of the colonic TLR/MyD88/NF-κB pathway. Supplementation with PCE improved intestinal morphology, and all doses of PCE significantly increased villus height (VH) in the ileum, whereas colonic crypt depth (CD) was significantly lower in the PCEH group than in the CON group. The PCEH diet significantly increased the levels of valeric and isovaleric acid in the colon content. Dietary PCEH also improved the colonic microbial community profile, reflected by a significant increase in Shannon's index compared with CON group. The abundance of Veillonellaceae and Rhodospirillales was significantly increased in the PCEH group at the family level. In conclusion, dietary PCE reduced diarrhoea rates, improved growth performance and enhanced immune function in weaned piglets. These improvements were potentially supported by altered ileum and colonic morphology, elevated colonic VFA levels, and modulation of colonic microbial profiles.

Metabolic and Microbial Profiling of Soil Microbial Community under Per- and Polyfluoroalkyl Substance (PFAS) Stress.

Per- and polyfluoroalkyl substances (PFAS) represent significant stress to organisms and are known to disrupt microbial community structure and function. Nevertheless, a detailed knowledge of the soil microbial community responding to PFAS stress at the metabolism level is required. Here we integrated UPLC-HRMS-based metabolomics data with 16S rRNA and ITS amplicon data across soil samples collected adjacent to a fluoropolymer production facility to directly identify the biochemical intermediates in microbial metabolic pathways and the interactions with microbial community structure under PFAS stress. A strong correlation between metabolite and microbial diversity was observed, which demonstrated significant variations in soil metabolite profiles and microbial community structures along with the sampling locations relative to the facility. Certain key metabolites were identified in the metabolite-PFAS co-occurrence network, functioning on microbial metabolisms including lipid metabolism, amino acid metabolism, and secondary metabolite biosynthesis. These results provide novel insights into the impacts of PFAS contamination on soil metabolomes and microbiomes. We suggest that soil metabolomics is an informative and useful tool that could be applied to reinforce the chemical evidence on the disruption of microbial ecological traits.

Inflammatory cytokines and a diverse cervicovaginal microbiota associate with cervical dysplasia in a cohort of Hispanics living in Puerto Rico.

Cervical cancer (CC) is women's fourth most common cancer worldwide. A worrying increase in CC rates in Hispanics suggests that besides Human papillomavirus infections, there may be other cofactors included in the epithelial microenvironment that could play a role in promoting the disease. We hypothesized that the cervical microbiome and the epithelial microenvironment favoring inflammation is conducive to disease progression in a group of Hispanics attending gynecology clinics in Puerto Rico. Few studies have focused on the joint microbiota and cytokine profile response in Hispanics outside the US, especially regarding the development of precancerous lesions. We aimed to investigate the relationship between the cervicovaginal microbiome and inflammation in Hispanic women living in PR while considering cervical dysplasia and HPV genotype risk. Cervical samples collected from 91 participants coming to gynecology clinics in San Juan, underwent 16S rRNA genes (V4 region) profiling, and cytokines were measured using Luminex MAGPIX technology. Cytokines were grouped as inflammatory (IL-1β, TNFα, IFNγ, IL-6), anti-inflammatory (IL- 4, IL-10, TGFβ1), and traffic-associated (IL-8, MIP1a, MCP1, IP10). They were related to microbes via an inflammation scoring index based on the quartile and tercile distribution of the cytokine's concentration. We found significant differences in the diversity and composition of the microbiota according to HPV type according to carcinogenic risk, cervical disease, and cytokine abundance. Community State Types (CSTs) represents a profile of microbial communities observed within the vaginal microbiome ecological niche, and Lactobacillus-depleted CST IV had ~ 90% dominance in participants with high-grade squamous intraepithelial lesions and high-risk HPV. The increasing concentration of pro-inflammatory cytokines was associated with a decrease in L. crispatus. In contrast, dysbiosis-associated bacteria such as Gardnerella, Prevotella, Atopobium concomitantly increased with pro-inflammatory cytokines. Our study highlights that the cervical microbiota of Hispanics living in Puerto Rico is composed mostly of diverse CST profiles with decreased Lactobacillus and is associated with a higher pro-inflammatory environment. The joint host-microbe interaction analyses via cytokine and microbiota profiling have very good translational potential.