Differences In Microbial Composition Research Articles

The Hidden Relationship between Intestinal Microbiota and Immunological Modifications in Preeclampsia Pathogenesis.

Preeclampsia is a multifactorial gestational syndrome characterized by increased blood pressure during pregnancy associated with multiorgan involvement. The impact of this disease on maternal and neonatal health is significant, as it can lead to various fetal comorbidities and contribute to the development of maternal comorbidities later in life. Consistent evidence has shown that the microbiota acts as a regulator of the immune system, and it may, therefore, influence the development of preeclampsia by modulating immune factors. This narrative review aims to investigate the role of the immune system in the pathogenesis of preeclampsia and to summarize the most recent literature on the possible link between preeclampsia and alterations in the intestinal microbiota. To this end, we conducted a literature search, aiming to perform a narrative review, on PubMed and Embase from January 1990 to March 2024, focusing on the latest studies that highlight the main differences in microbial composition between patients with and without preeclampsia, as well as the effects of microbial metabolites on the immune system. From the review of 28 studies assessing the intestinal microbiota in preeclamptic women, preeclampsia could be associated with a state of dysbiosis. Moreover, these patients showed higher plasmatic levels of endotoxin, pro-inflammatory cytokines, and T helper 17 cells; however, the findings on specific microbes and metabolites that could cause immune imbalances in preeclampsia are still preliminary.

Alterations of gut microbiome in eosinophilic chronic rhinosinusitis.

A growing body of evidence has elucidated that the gut microbiota has a crucial impact on the pathophysiological process of atopic diseases. Eosinophilic chronic rhinosinusitis with nasal polyps (eCRSwNP) is a local atopic disease of the systemic immune response. Alterations in the gut microbiome in eCRSwNP patients remain largely undefined. 16S rRNA gene sequencing was performed in a cross-sectional study of 17 eCRSwNP patients, 9 noneCRSwNP patients and 13 healthy controls, and gut microbiota DNA sequencing between each pair of groups was compared using bioinformatic methods. Compared with that of healthy controls, the gut microbiomes of eCRSwNP patients were characterised by a distinct overall microbial composition. However, no significant differences were found in the alpha diversity of the gut microbiota between patients and healthy controls. The distinct differences in microbial composition were significantly correlated with the severity of disease. At the genus level, the abundance of Faecalibacterium positively correlated with Lund-Mackay CT scores. Similarly, the abundance of Turicibacter positively correlated with the percentage of tissue eosinophils. We found alterations in the gut microbiome in eCRSwNP patients, and the alterations in the gut microbiome were correlated with the severity of disease.

Mosquitoes reared in distinct insectaries within an institution in close spatial proximity possess significantly divergent microbiomes.

The microbiome affects important aspects of mosquito biology and differences in microbial composition can affect the outcomes of laboratory studies. To determine how the biotic and abiotic conditions in an insectary affect the composition of the bacterial microbiome of mosquitoes we reared mosquitoes from a single cohort of eggs from one genetically homogeneous inbred Aedes aegypti colony, which were split into three batches, and transferred to each of three different insectaries located within the Liverpool School of Tropical Medicine. Using three replicate trays per insectary, we assessed and compared the bacterial microbiome composition as mosquitoes developed from these eggs. We also characterised the microbiome of the mosquitoes' food sources, measured environmental conditions over time in each climate-controlled insectary, and recorded development and survival of mosquitoes. While mosquito development was overall similar between all three insectaries, we saw differences in microbiome composition between mosquitoes from each insectary. Furthermore, bacterial input via food sources, potentially followed by selective pressure of temperature stability and range, did affect the microbiome composition. At both adult and larval stages, specific members of the mosquito microbiome were associated with particular insectaries; and the insectary with less stable and cooler conditions resulted in slower pupation rate and higher diversity of the larval microbiome. Tray and cage effects were also seen in all insectaries, with different bacterial taxa implicated between insectaries. These results highlight the necessity of considering the variability and effects of different microbiome composition even in experiments carried out in a laboratory environment starting with eggs from one batch; and highlights the impact of even minor inconsistencies in rearing conditions due to variation of temperature and humidity.

Exploring the Microbial Diversity and Composition of Three Cigar Product Categories

Cigars and cigarillos are emerging as popular tobacco alternatives to cigarettes. However, these products may be equally harmful to human health than cigarettes and are associated with similar adverse health effects. We used 16S rRNA gene amplicon sequencing to extensively characterize the microbial diversity and investigate differences in microbial composition across 23 different products representing three different cigar product categories: filtered cigar, cigarillo, and large cigar. High throughput sequencing of the V4 hypervariable region of the 16 s rRNA gene revealed 2124 Operational Taxonomic Units (OTUs). Our findings showed that the three categories of cigars differed significantly in observed richness and Shannon diversity, with filtered cigars exhibiting lower diversity compared to large cigars and cigarillos. We also found a shared and unique microbiota among different product types. Firmicutes was the most abundant phylum in all product categories, followed by Actinobacteria. Among the 16 genera shared across all product types were Bacillus, Staphylococcus, Pseudomonas, and Pantoea. Nine genera were exclusively shared by large cigars and cigarillos and an additional thirteen genera were exclusive to filtered cigars. Analysis of individual cigar products showed consistent microbial composition across replicates for most large cigars and cigarillos while filtered cigars showed more inter-product variability. These findings provide important insights into the microbial diversity of the different cigar product types.

Analysis of nasopharyngeal microbiota revealing microbial disturbance associated with ovine respiratory complex

The ovine respiratory complex (ORC) is a complex respiratory disease process in ovine causing a significant health concern with substantial morbidity and mortality. It poses a significant threat of impacting animal health, leading to severe health consequences and considerable economic loss. Research on the upper respiratory tract (URT) microbiota is critical for offering insights into pathogenesis, prevention, and treatment strategies of ORC. The goal of this study is to compare the nasopharyngeal microbiota of clinically healthy Hu sheep (Group H) and sheep with ORC (Group P). The 16S rDNA gene amplicon high-throughput sequencing technique was applied to identify the microbial composition in the nasopharyngeal samples. The results showed that there was no significant difference in the microbiota diversity and richness between ORC and healthy sheep. However, there were significant differences in microbial composition, such as the relative abundance of Enterobacteriaceae, Moraxellaceae, Pasteurellaceae, and Streptococcaceae between the two groups. The abundance of aerobes in sheep with ORC increased significantly, while the abundance of anaerobes and facultative anaerobes decreased significantly. There were also differences in the taxa phenotypes associated with biofilm forming, mobile element-containing, oxidative stress-tolerance, and potential pathogens between the two groups. Our study showed the nasopharyngeal microbiota composition and its associated shifts between clinically healthy sheep and ORC sheep in China. These findings suggest that shifts in the nasopharyngeal microbiota could be a contributing factor to the pathogenesis of ORC, offering a potential avenue for the development of targeted interventions and treatments for this condition in sheep.

Adult Outpatients with Long COVID Infected with SARS-CoV-2 Omicron Variant. Part 1: Oral Microbiota Alterations

BackgroundMany individuals experience long COVID after SARS-CoV-2 infection. As microbiota can influence health, it may change with COVID-19. This study investigated differences in oral microbiota between COVID-19 patients with and without long COVID. MethodsBased on a prospective follow-up investigation, this nested case-control study evaluated the differences in oral microbiota in individuals with and without long COVID (Symptomatic and Asymptomatic groups), which were assessed by 16S rRNA sequencing on tongue coating samples. A predictive model was established using machine learning based on specific differential microbial communities. ResultsOne-hundred-and-eight patients were included (n=54 Symptomatic group). The Symptomatic group had higher Alpha diversity indices (observed_otus, Chao1, Shannon, and Simpson indices), differences in microbial composition (Beta diversity), and microbial dysbiosis with increased diversity and relative abundance of pathogenic bacteria. Marker bacteria (c__Campylobacterota, o__Coriobacteriales, o__Pseudomonadales, and o__Campylobacterales) were associated with long COVID by linear discriminant analysis effect size and receiver operating characteristic curves (AUC 0.821). ConclusionThere were distinct variations in oral microbiota between COVID-19 patients with and without long COVID. Changes in oral microbiota may indicate long COVID.

Meta-analysis identifies common gut microbiota associated with multiple sclerosis

BackgroundPrevious studies have identified a diverse group of microbial taxa that differ between patients with multiple sclerosis (MS) and the healthy population. However, interpreting findings on MS-associated microbiota is challenging, as there is no true consensus. It is unclear whether there is gut microbiota commonly altered in MS across studies.MethodsTo answer this, we performed a meta-analysis based on the 16S rRNA gene sequencing data from seven geographically and technically diverse studies comprising a total of 524 adult subjects (257 MS and 267 healthy controls). Analysis was conducted for each individual study after reprocessing the data and also by combining all data together. The blocked Wilcoxon rank-sum test and linear mixed-effects regression were used to identify differences in microbial composition and diversity between MS and healthy controls. Network analysis was conducted to identify bacterial correlations. A leave-one-out sensitivity analysis was performed to ensure the robustness of the findings.ResultsThe microbiome community structure was significantly different between studies. Re-analysis of data from individual studies revealed a lower relative abundance of Prevotella in MS across studies, compared to controls. Meta-analysis found that although alpha and beta diversity did not differ between MS and controls, a higher abundance of Actinomyces and a lower abundance of Faecalibacterium were reproducibly associated with MS. Additionally, network analysis revealed that the recognized negative Bacteroides-Prevotella correlation in controls was disrupted in patients with MS.ConclusionsOur meta-analysis identified common gut microbiota associated with MS across geographically and technically diverse studies.

Chloroquine Downregulation of Intestinal Autophagy Changed Intestinal Microbial Community Compositions and Metabolite Profiles in Piglets.

Our previous study demonstrated that moderate inhibition of intestinal autophagy was beneficial to alleviate early weaning stress in piglets, but the detailed mechanism behind this was unclear. Microbiota-mediated enterocyte autophagy helps maintain intestinal homeostasis. This study investigated the effects of inhibition or activation of autophagy in intestinal microbial community compositions and metabolite profiles in piglets. Eighteen 24-day-old weaned piglets were divided into three groups (each treatment of six piglets) and treated daily with rapamycin (RAPA), chloroquine (CQ) or a control volume of normal saline (CON group). Before the formal trial, the piglets were allowed to acclimatize for 3 days, and then the trial period was 14 days. Collected samples from the ileum and colon underwent 16S rRNA gene sequencing and metabolite analysis. Significant differences in microbial composition were observed in both the ileum and colon of the RAPA and CQ groups compared to the CON group (p < 0.05). In addition, the relative levels of abundance of Peptostreptococcus, Fusobacterium, Dialister, Selenomonas and Oceanobacillus in the ileum and Porphyromonas, Bacteroides, unidentified_Lachnospiraceae, Akkermansia, Sharpea, Peptococcus, Pseudoalteromonas, Peptoclostridium and unidentified_Acidobacteria in the colon were improved in piglets fed the RAPA diet, whereas the relative levels of abundance of Turicibacter, Rickettsiella and Sarcina in the ileum and Roseburia and Kroppenstedtia in the colon were enhanced in the CQ group (p < 0.05). Meanwhile, metabolomic analysis showed that there were significant differences in metabolites among all groups (p < 0.05), and KEGG enrichment analysis revealed that differential metabolites were mainly enriched in the ABC transporters and biosynthesis of amino acids pathways. Furthermore, these metabolites were closely related to differential microorganisms (p < 0.05). Overall, autophagy inhibition regulates the composition of intestinal microorganisms and their metabolites, and these differential metabolites are significantly correlated with differential intestinal microorganisms, which may in turn affect the production performance of weaned piglets.

Profiling of bacterial community’s dynamics inhibiting the intestinal tract of broiler chickens growing in naturally ventilated house

An experiment was conducted to evaluate the relative abundance of gastrointestinal microbial structures in different gut sections of Cobb500 broiler chickens reared in naturally ventilated houses and fed a standard diet for 35 days under the ambient environment of Oman. In this research, sequences from 1,179,068 16S rDNA analyses were grouped into 253 operational taxonomic units with a sequence similarity threshold of 97%. These units revealed the presence of seven phyla and twenty-six families. Firmicutes were found to be the dominant phylum in the duodenum (96.4%), jejunum (88.8%), ileum (96.8%), and cecum (96.8%). In contrast, Tenericutes and Thermi were the least prevalent phyla across these gut regions, accounting for between 0.01% and 0.12% of the total sequences. Actinobacteria, Bacteroidetes, and Cyanobacteria showed higher prevalence in the cecum (accounted for 6.59%, 7.42%, and 7.50%, respectively) than in duodenum, jejunum, and ileum. Lactobacillaceae were notably observed as the predominant family in the four gut segments, accounting for 73.87% in the duodenum, 43.30% in the jejunum, 77.81% in the ileum, and 46.30% in the caecum, collectively comprising a substantial portion of the sequencing data. Lachnospiraceae and Ruminococcaceae emerged as dominant families, comprising 28.61% and 30.8% of the sequencing data across all four intestinal sections, respectively. Statistical analysis of the 16S rDNA libraries showed that each section of the intestine contains a unique bacterial community with an increase in bacterial diversity parallel to age increase. The study's findings reveal the temporal dynamics of the chicken's gut microbiota in a naturally ventilated housing environment. The results obtained provide a unique perspective on the diversity of bacterial communities, highlighting significant differences in microbial composition across different segments of the intestine and offering practical insights for the management of broiler chicken health.

Variations in soil microbial communities in different saline soils under typical Populus spp. vegetation in alpine region of the Qaidam Basin, NW China

Salinization is a severe threat to agriculture and the environment in many areas, and the same in Qaidam Basin, Qinghai Province, Northwestern China. Microorganisms have an important influence on regulating the biochemical cycles of ecosystems; however, systematic research exploring microbial diversity and interactions with saline-soil ecosystems’ environmental variables remains scarce. Thus, 16 S rRNA high-throughput sequencing was performed in this paper to characterize microbial diversity under different levels of salinized soils: non-salinized (NS, 2.25 g/L), moderately salinized (MS, 6.14 g/L) and highly salinized (HS, 9.82 g/L). The alpha diversity results showed that the HS soil was significantly different from the NS and MS soils. An analysis of similarity (ANOSIM) and a principal co-ordinates analysis (PCoA) indicated that NS and MS clustered closely while HS separated from the other two. Significant differences in microbial composition were observed at the taxonomic level. Proteobacteria (42.29–79.23 %) were the most abundant phyla in the studied soils. Gammaproteobacteria (52.49 and 66.61 %) had higher abundance in the MS and HS soils at the class level; Methylophaga and Pseudomonas were the predominant bacteria in the HS soil; and Azotobacter and Methylobacillus were abundant in the MS soil. Most genera belonging to Proteobacteria and Actinobacteria were detected via a linear discriminate analysis (LDA) effect size (LEfSe) analysis, which indicated that microbes with the ability to degrade organic matter and accomplish nutrient cycling can be well-adapted to salt conditions. Further analyses (redundancy analysis and Mantel test) showed that the microbial communities were mainly related to the soil salinity, electrical conductivity (EC1:5), total phosphorus (TP) and ammonia nitrogen (NH4+-N). Overall, the findings of the study can provide insights for better understanding the dominant indigenous microbes and their roles in biochemical cycles in different saline soils in the Qaidam Basin, Qinghai Province, China. The researches related to microbial community under typical poplar species should further clarify the mechanism of plant-microbial interaction and benefit for microbial utilization in salt soil remediation.

O-268 Re-considering the endometrial microbiome: a comparison of DNA- and RNA-based sequencing techniques within the same cohort

Abstract Study question Does the analysis of the endometrial microbiome provide the same information when using DNA or RNA sequencing-based techniques? Summary answer DNA vs. RNA-based microbiome analysis techniques demonstrate significant microbial compositional differences, meaning that the previous endometrial 16S rRNA gene-based microbiome analysis results might be overestimated. What is known already In recent years, high-throughput sequencing technologies have revolutionised the field of reproductive microbiome research. Our understanding of the composition of endometrial microbiome predominantly relies on DNA-based 16S rRNA gene profiling method. Regardless of its effectiveness and low cost, its underestimation of microbial diversity, abundance, or functionality and lack of detection precision on species level have been highlighted. The meta-transcriptome analysis, RNA-based method, overcomes these limitations and identifies functional genes that are actively expressed by the alive microbes. This study aims to elucidate for the first time the endometrial microbiome using a dual approach of 16S rRNA gene-method and meta-transcriptomic analyses. Study design, size, duration In total forty-seven women with infertility at ages 27-42 years old were enrolled in the present study. Paired endometrial samples, endometrial brushing and Pipelle biopsy were collected from each participant at the mid-secretory menstrual phase (LH + 7/9). Participants/materials, setting, methods Endometrial samples were collected using Tao Brush for 16S rRNA analysis (DNA analysis) and Pipelle endometrial curette for meta-transcriptomic analysis (total RNA analysis). QIAamp UCP Pathogen Mini Kit was used for DNA extraction and 16S rRNA gene V3-V4 regions were sequenced on MiSeq. RNA was extracted using miRNeasy Micro kit, with rRNA removal by RiboZero kit and Libraries were generated using Stranded Total RNA Prep. Taxonomy was assigned by using Kraken2 (v2.2.1), Bracken (v2.7). Main results and the role of chance To the best of our knowledge, this is the first study to compare endometrial microbial identification using both metagenomics (16S rRNA sequencing) and meta-transcriptomics (meta-RNA sequencing) within the same cohort. Analysis of the composition of the microorganisms by bacterial 16S rRNA gene sequencing revealed that the most abundant bacterial genus in the endometrium was Lactobacillus. In the meta-transcriptome analysis, no microorganisms belonging to the Lactobacillus genus were detected in high abundance. This indicates that the relative abundance of this genus at the DNA level does not necessarily imply microbial activity or the presence of viable Lactobacillus in the endometrium. The meta-transcriptomics analysis detected microbial taxa such as Staphylococcus, Bacillus, Streptococcus, and Burkholderia as the most dominant. The results suggest that DNA-based detection of microorganisms in the endometrium may be overestimated due to the presence of naked DNA sequences or microorganisms from the vagina and cervix. Furthermore, RNA-based analysis demonstrates a population of active microorganisms different from the image shown by DNA analysis. Altogether, our study results indicate that the uterine microenvironment, as previously identified through DNA sequencing, may partly reflect the vaginocervical microenvironment, with the uterine tissue being a low biomass site not dominated by lactobacilli. Limitations, reasons for caution The endometrial samples were paired; however, DNA was analysed in the endometrial brushing sample while RNA in the tissue biopsy, which might result in some differences in microbial composition. Wider implications of the findings Contrary to the general belief of the Lactobacillus dominance in the human endometrium, our study suggests that the endometrial microenvironment may be harbouring DNA fragments and/or cells of lactobacilli originating from the lower reproductive tract. Our study results call out to re-consider/re-analyse the endometrial microbiome in health and disease. Trial registration number not applicable

O-281 Characterization of Vaginal microbiota and reproductive outcomes associated with assisted reproductive technologies through next-generation sequencing, from Indian population

Abstract Study question Is there any association between the composition of the vaginal microbiota and the reproductive outcomes in infertile women’s undergoing for assisted reproductive treatments (ART)? Summary answer Higher microbial abundance in non-pregnant patients compared to pregnant patients. These pathogens could be used as a possible marker for a higher IVF failure rate. What is known already Various next- generation sequencing methods have been used to study bacterial populations in infertile Women. Vaginal microbiota could have an influence on success rates of fertility treatments. The bacterial microbiota varies by the population. There is no direct evidence on this subject to guide clinical decision making or its influence on the hierarchy of fertility treatments. While the presence of pathogenic bacteria non-Lactobacilli dominated microbiota is associated with poor reproductive outcomes in assisted reproductive treatments (ART). Additional studies, particularly those using metagenomics approaches, may be useful. Study design, size, duration A total of 240 infertile women’s were included in the study. The study population consists of patients attending to the ART unit of a tertiary medical center Udaipur, India, between November 2021 to October 2023. Depending on the biochemical pregnancy results, they were divided into two groups. Group 1 (n = 128) was pregnancy (P), and Group 2 (n = 112) non- pregnancy (NP) group, Patients were aged between (20-45 years). The ethical approval was obtained from the institute. Participants/materials, setting, methods DNA was extracted from vaginal swab samples collected at the time of oocyte pick up using the commercially available ( DNeasy Power Soil kit). The Vaginal microbiota of samples were analyzed using 16S ribosomal RNA gene amplification (MinION) Oxford Nanopore Ltd. Bioinformatics analysis was performed using QIIME2 and Microbiome Analyst packages. Alpha, beta diversity and taxonomic characterization were compared for microbial composition. The findings of the principle coordinate analysis were shown using R version 4.0. Main results and the role of chance Our results show that higher Shannon and Simpson index were obtained in the non- pregnancy (NP) group compared to the pregnancy (P) group. In addition, the partial least squares discriminant analysis (PLS-DA) revealed a difference in microbial composition between pregnancies (P) and non- pregnancy (NP) groups, as well as a higher microbial abundance in non-pregnant patients compared to pregnant patients. At the phylum level Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, and Bacteroidetes are the most common predominant in the pregnancy (P) group (80.77, 9.52, 9.18, 0.04, and 0.40%, respectively) and the non- pregnancy (NP) group (72, 61, 12.41, 8.01, and 3.75%). A higher abundance of Firmicutes (80.77 vs. 72.61%) and Proteobacteria (9.18 vs. 8.01%), and a lower abundance of Actinobacteria (9.52 vs. 12.41%, p = 0.03), Fusobacteria (0.04 vs. 8.01%, p = 0.02), and Bacteroidetes (0.40 vs. 3.75%, p = 0.03) were observed in pregnancy (P) group. At the genus level, pregnancy group (P) increased the abundance of probiotics lactic acid bacteria (74.61 vs 63.09%) and decreased the abundance of the pathogen Gardnerella (6.03 vs 7.24%, p = 0.03), Atopobium (0.84 vs 4.14%, p = 0.02), Sneathia (0.03 vs. 3.75%, p = 0.02), and Prevotella (0.38 vs. 3, 02%, p = 0.04). Limitations, reasons for caution The limited sample size is the primary constraint of this study. Larger studies with a larger sample size are needed to confirm the distinct microbiome patterns identified in female reproductive tracts samples in connection to infertility and live birth rate (LBR) outcomes. Wider implications of the findings Vaginal microbiota composition associated to different clinical outcomes in patients undergoing ART might have profound implications. This may lead to failed fertility treatments and reduced live birth rate (LBR). More studies are needed to clarify the relative effectiveness of treatments for infertility. Trial registration number NA

16S rRNA sequencing reveals microbiota differences in orthopedic implants between aseptic loosening and prosthetic joint infection cases.

Prosthetic joint infection (PJI) and aseptic loosening (AL) are common complications of total joint arthroplasty. An accumulation of evidence indicates the presence of microbial communities on prosthetic implants, but the overall microbial profile is unclear. In this study, we aimed to investigate the differences in the microbial composition of prosthetic implants obtained from PJI and AL patients using the 16S rRNA sequencing method. Patients who underwent revision hip, knee, or shoulder arthroplasty caused by PJI (n = 20) or AL (n = 10) were enrolled in the study. 16S rRNA sequencing targeting the V3-V4 region was performed on the microbial specimens collected from synovial fluid, periprosthetic deep-tissue, and biofilm during the revision surgery. The sequenced raw data were analysed for microbial composition and ecological and differential abundance analyses using bioinformatics tools. The AL group had relatively balanced and higher diversity, with Staphylococcus, Streptococcus, and Veillonella being prominent. In the PJI group, Staphylococcus and Pseudomonas were predominant, especially in deep-tissue samples and biofilm samples, respectively. The differential abundance analysis identified 15 and 2 distinctive taxa in the AL and PJI groups, respectively. Our findings provided preliminary insights supporting the existence of periprosthetic microbiota in orthopedic implants and explaining the differences in microbial composition between the AL and PJI groups.

The Human Microbiome-A Physiologic Perspective.

The human microbiome consists of the microorganisms associated with the body, such as bacteria, fungi, archaea, protozoa, and viruses, along with their gene content and products. These microbes are abundant in the digestive, respiratory, renal/urinary, and reproductive systems. While microbes found in other organs/tissues are often associated with diseases, some reports suggest their presence even in healthy individuals. Lack of microbial colonization does not indicate a lack of microbial influence, as their metabolites can affect distant locations through circulation. In a healthy state, these microbes maintain a mutualistic relationship and help shape the host's physiological functions. Unlike the host's genetic content, microbial gene content and expression are dynamic and influenced by factors such as ethnicity, genetic background, sex, age, lifestyle/diet, and psychological/physical conditions. Therefore, defining a healthy microbiome becomes challenging as it is context dependent and can vary over time for an individual. Although differences in microbial composition have been observed in various diseases, these changes may reflect host alterations rather than causing the disease itself. As the field is evolving, there is increased emphasis on understanding when changes in the microbiome are an important component of pathogenesis rather than the consequence of a disease state. This article focuses on the microbial component in the digestive and respiratory tracts-the primary sites colonized by microorganisms-and the physiological functions of microbial metabolites in these systems. It also discusses their physiological functions in the central nervous and cardiovascular systems, which have no microorganism colonization under healthy conditions based on human studies. © 2024 American Physiological Society. Compr Physiol 14:5491-5519, 2024.

Analysis of differences in the rumen microbiome and metabolic function in prepartum dairy cows with different body condition scores

BackgroundThe rumen is a crucial digestive organ for dairy cows. The rumen microbiota assists in the digestion of plant feed through microbe-mediated fermentation, during which the plant feed is transformed into nutrients for the cow's use. Variations in the composition and function of the rumen microbiome affect the energy utilization efficiency of dairy cows, which is one of the reasons for the varying body condition scores (BCSs). This study focused on prepartum Holstein dairy cows to analyze differences in rumen microbiota and metabolites among cows with different BCSs. Twelve prepartum dairy cows were divided into two groups, low BCS (LBCS, BCS = 2.75, n = 6) and high BCS (HBCS, BCS = 3.5, n = 6), to explore differences in microbial composition and metabolites.ResultsIn the HBCS group, the genera within the phylum Firmicutes exhibited stronger correlations and greater abundances. Phyla such as Firmicutes, Patescibacteria, Acidobacteriota, Euryarchaeota, and Desulfobacterota, in addition to most of their constituent microbial groups, were significantly more abundant in the HBCS group than in the LBCS group. At the genus level, the abundances of Anaerovibrio, Veillonellaceae_UCG_001, Ruminococcus_gauvreauii_group, Blautia, Eubacterium, Prevotellaceae_YAB2003_group, Schwartzia, and Halomonas significantly increased in the HBCS group. The citrate cycle, involved in carbohydrate metabolism, exhibited a significant enrichment trend, with a notable increase in the abundance of its key substrate, citrate, in the HBCS group. This increase was significantly positively correlated with the differential bacterial genera.ConclusionIn this study, prepartum dairy cows with higher BCS exhibited greater abundance of Firmicutes. This study provides theoretical support for microbiological research on dairy cows with different BCSs and suggests that regulating the rumen microbiome could help maintain prepartum dairy cows within an optimal BCS range.

Adolescent alcohol use is associated with differences in the diversity and composition of the oral microbiome.

Adolescence is a sensitive stage of oral microbial development that often coincides with the initiation and escalation of alcohol use. Thus,adolescents may be particularly susceptible to alcohol-induced alterations in the oral microbiome, though minimal research has been done in this area. Understanding the connection between the oral microbiome and alcohol use during adolescence is important to understand fully the biological consequences of alcohol use to mitigate potential adverse outcomes. Saliva samples were collected from adolescents aged 17-19 who used alcohol heavily (n = 21, 52.4% female) and those who did not use alcohol or any other substances (n = 18, 44.4% female). We utilized 16S rRNA sequencing to examine differences in microbial diversity and composition between the groups. Foralpha diversity, evenness was significantly lower in the drinking group than the control group as indicated by Pielou's evenness, Shannon, and Simpson indices. There were no statistically significant findings for beta diversity. Differential abundance analyses revealed higher abundances of Rothia and Corynebacterium in the alcohol-using group using both centered-log-ratio and relative abundance normalization. These genera are known for their high capacity to convert alcohol into acetaldehyde, a toxic metabolite reported to play a role in the neurobiological effects of alcohol. An unclassified Clostridia UCG-014, Streptobacillus, Comamonas, unclassified Lachnospiraceae, and Parvimonas were also identified as significantly different between groups when using only one of the normalization techniques. This is the first study designed specifically to compare the oral microbiome of adolescents who use alcohol with that of control participants. Our findings reveal distinct alcohol-related differences in microbial composition and taxon abundance, emphasizing the importance of understanding the impact onthe oral microbiome of alcohol use during adolescence. Because the oral microbiome is malleable, this study provides foundational work for future prevention and intervention studies.

16S rRNA gene sequencing reveals altered gut microbiota in young adults with schizophrenia and prominent negative symptoms.

Gut dysbiosis has been established as a characteristic of schizophrenia (SCH). However, the signatures regarding SCH patients with prominent negative symptoms (SCH-N) in young adults have been poorly elucidated. Stool samples were obtained from 30 young adults with SCH-N, 32 SCH patients with prominent positive symptoms (SCH-P) along with 36 healthy controls (HCs). Microbial diversity and composition were analyzed by 16S rRNA gene sequencing. Meanwhile, psychiatric symptoms were assessed by the positive and negative syndrome scale (PANSS). There is a significant difference in β-diversity but not α-diversity indexes among the three groups. Moreover, we found a higher abundance of Fusobacteria and Proteobacteria phyla and a lower abundance of Firmicutes phyla in SCH-N when compared with HC. Besides, we identified a diagnostic potential panel comprising six genera (Coprococcus, Monoglobus, Prevotellaceae_NK3B31_group, Escherichia-Shigella, Dorea, and Butyricicoccus) that can distinguish SCH-N from HC (area under the curve=0.939). However, the difference in microbial composition between the SCH-N and SCH-P is much less than that between SCH-N and the HC, and SCH-N and SCH-P cannot be effectively distinguished by gut microbiota. The composition of gut microbiota was changed in the patients with SCH-N, which may help in further understanding of pathogenesis in young adults with SCH-N.

The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study

BackgroundThe human gut microbiome (GM) is involved in inflammation and immune response regulation. Dysbiosis, an imbalance in this ecosystem, facilitates pathogenic invasion, disrupts immune equilibrium, and potentially triggers diseases including various human leucocyte antigen (HLA)-B27-associated autoinflammatory and autoimmune diseases such as inflammatory bowel disease (IBD) and spondyloarthropathy (SpA). This study assesses compositional and functional alterations of the GM in patients with HLA-B27-associated non-infectious anterior uveitis (AU) compared to healthy controls.MethodsThe gut metagenomes of 20 patients with HLA-B27-associated non-infectious AU, 21 age- and sex-matched HLA-B27-negative controls, and 6 HLA-B27-positive healthy controls without a history of AU were sequenced using the Illumina NovaSeq 6000 platform for whole metagenome shotgun sequencing. To identify taxonomic and functional features with significantly different relative abundances between groups and to identify associations with clinical metadata, the multivariate association by linear models (MaAsLin) R package was applied.ResultsSignificantly higher levels of the Eubacterium ramulus species were found in HLA-B27-negative controls (p = 0.0085, Mann-Whitney U-test). No significant differences in microbial composition were observed at all other taxonomic levels. Functionally, the lipid IVA biosynthesis pathway was upregulated in patients (p < 0.0001, Mann-Whitney U-test). A subgroup analysis comparing patients with an active non-infectious AU to their age- and sex-matched HLA-B27-negative controls, showed an increase of the species Phocaeicola vulgatus in active AU (p = 0.0530, Mann-Whitney U-test). An additional analysis comparing AU patients to age- and sex-matched HLA-B27-positive controls, showed an increase of the species Bacteroides caccae in controls (p = 0.0022, Mann-Whitney U-test).ConclusionIn our cohort, non-infectious AU development is associated with compositional and functional alterations of the GM. Further research is needed to assess the causality of these associations, offering potentially novel therapeutic strategies.

Characterization of pediatric urinary microbiome at species-level resolution indicates variation due to sex, age, and urologic history

Recently, associations between recurrent urinary tract infections (UTI) and the urinary microbiome (urobiome) composition have been identified in adults. However, little is known about the urobiome in children. We aimed to characterize the urobiome of children with species-level resolution and to identify associations based on UTI history. Fifty-four children (31 females and 21 males) from 3 months to 11 years of age participated in the study. Catheterized urine specimens were obtained from children undergoing a clinically indicated voiding cystourethrogram. To improve the analysis of the pediatric urobiome, we used a novel protocol using filters to collect biomass from the urine coupled with synthetic long-read 16S rRNA gene sequencing to obtain culture-independent species-level resolution data. We tested for differences in microbial composition between sex and history of UTIs using non-parametric tests on individual bacteria and alpha diversity measures. We detected bacteria in 61% of samples from 54 children (mean age 40.7 months, 57% females). Similar to adults, urobiomes were distinct across individuals and varied by sex. The urobiome of females showed higher diversity as measured by the inverse Simpson and Shannon indices but not the Pielou evenness index or number of observed species (p=0.05, p=0.04, p=0.35, and p=0.11, respectively). Additionally, several species were significantly overrepresented in females compared to males, including those from the genera Anaerococcus, Prevotella, and Schaalia (p=0.03, 0.04, and 0.02, respectively). Urobiome diversity increased with age, driven mainly by males. Comparison of children with a history of 1, 2, or 3+ UTIs revealed that urobiome diversity significantly decreases in the group that experienced 3+ UTIs as measured by the Simpson, Shannon, and Pielou indices (p=0.03, p=0.05, p=0.01). Several bacteria were also found to be reduced in abundance. In this study, we confirm that urobiome can be identified from catheter-collected urine specimens in infants as young as 3 months, providing further evidence that the pediatric bladder is not sterile. In addition to confirming variations in the urobiome related to sex, we identify age-related changes in children under 5 years of age, which conflicts with some prior research. We additionally identify associations with a history of UTIs. Our study provides additional evidence that the pediatric urobiome exists. The bacteria in the bladder of children appear to be affected by early urologic events and warrants future research.

Screening, identification and evaluation of an acidophilic strain of Bacillus velezensis B4-7 for the biocontrol of tobacco bacterial wilt.

Tobacco (Nicotiana tabacum L.) bacterial wilt, caused by Ralstonia solanacearum, is indeed a highly destructive plant disease, leading to substantial damage in tobacco production. While biological control is considered an effective measure for managing bacterial wilt, related research in this area has been relatively limited compared to other control methods. In order to discover new potential antagonistic bacteria with high biocontrol efficacy against tobacco bacterial wilt, we conducted an analysis of the microbial composition differences between disease-suppressive and disease-conducive soils using Illumina sequencing. As a result, we successfully isolated six strains from the disease-suppressive soil that exhibited antibacterial activity against Ralstonia solanacearum. Among these strains, B4-7 showed the strongest antibacterial activity, even at acidic conditions with a pH of 4.0. Based on genome analysis using Average Nucleotide Identity (ANI), B4-7 was identified as Bacillus velezensis. In greenhouse and field trials, strain B4-7 significantly reduced the disease index of tobacco bacterial wilt, with control efficiencies reaching 74.03% and 46.88% respectively. Additionally, B4-7 exhibited plant-promoting abilities that led to a 35.27% increase in tobacco production in field conditions. Quantitative real-time (qPCR) analysis demonstrated that strain B4-7 effectively reduced the abundance of R. solanacearum in the rhizosphere. Genome sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed that strain B4-7 potentially produces various lipopeptide metabolites, such as microlactin, bacillaene, difficidin, bacilysin, and surfactin. Furthermore, B4-7 influenced the structure of the rhizosphere soil microbial community, increasing bacterial abundance and fungal diversity, while also promoting the growth of different beneficial microorganisms. In addition, B4-7 enhanced tobacco's resistance to R. solanacearum by increasing the activities of defense enzymes, including superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL), peroxidase (POD), catalase (CAT), and polyphenol oxidase (PPO). Collectively, these findings suggest that B. velezensis B4-7 holds significant biocontrol potential and can be considered a promising candidate strain for eco-friendly management of tobacco bacterial wilt.