Differences In Beta Diversity Research Articles

Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome.

The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.

Altered Urine Microbiome in Male Children and Adolescents with Attention-Deficit Hyperactivity Disorder.

While interest in developing the human microbiome as a biomarker for attention-deficit hyperactivity disorder (ADHD) is increasing, there has been limited exploration in utilizing urine samples. In this study, we analysed urine microbiome profiles by extracting 16S ribosomal DNA from purified bacteria-derived extracellular membrane vesicles obtained from urine samples. Sequencing libraries were constructed by amplifying V3-V4 hypervariable regions sequenced using Illumina MiSeq. Profiles of male Korean children and adolescents with ADHD (n = 33) were compared with healthy sex-matched controls (n = 39). Statistically controlling for age, we found decreased alpha diversity in the urine bacteria of the ADHD group, as evidenced by reduced Shannon and Simpson indices (p < 0.05), and significant differences in beta diversity between the two groups (p < 0.001). The phyla Firmicutes and Actinobacteriota, as well as the genera Ralstonia and Afipia, were relatively more abundant in the ADHD group. The phylum Proteobacteria and the genera Corynebacterium and Peptoniphilus were more abundant in the control group. Notably, the genus Afipia exhibited significant correlations with the Child Behavior Checklist Attention Problems score and DSM-oriented ADHD subscale. This study is the first to propose the urine microbiome as a potential biomarker for pediatric ADHD.

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars.

Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.

Characteristic of upper respiratory tract microbiota in severe covid-19 adult patients in Indonesia

Introduction: Nowadays, new cases of COVID-19 have been found with severe cases and deaths. The upper respiratory microbiota has been associated with susceptibility to viral infection and disease severities. However, the association of respiratory tract microbiota with the modulation of COVID-19 outcomes still raises a question. Therefore, we examined the association between the diversity of upper respiratory microbiota and clinical manifestations of COVID-19. Methods: This research is an observational cross-sectional study. We characterized the microbiota in the upper airway using the 16S ribosomal RNA sequencing method in 74 COVID-19 patients aged 18-64 years. We also examined the association between COVID-19 severities with alpha and beta diversity of upper respiratory microbiota. The alpha and beta diversity was analyzed by QIIME and shown by R software, AMOVA and MRPP testing was done with R software. The t test and diagrams were performed using R software. Bivariate analysis was carried out by t-test and Chi-square test. Results: The top five phyla in the upper respiratory tract of Indonesian COVID-19 patients with age 18-64 years old were Firmicutes (32,3%), Bacteroidota (27,1%), Fusobacteriota (15,2%), Proteobacteria (15,1%) and Actinobacteria (7,1%). Shannon and ACE index analysis showed no decline of microbiota diversity in the upper airway with increased disease severity. However, there were significant beta diversity differences in the upper airway microbiota between mild and severe COVID-19. The Firmicutes phylum and Oribacterium genus abundance were significantly higher in severe COVID-19 than in mild. The quantity of the Fusobacteriota phylum, Neisseria, and Fusobacterium genera was significantly higher in mild COVID-19 than in severe. Conclusion: Our research supports the relationship between the severity of COVID-19 and the diversity of the microbiota in the upper airway in adults. Further studies are needed to examine how microbiota prevents COVID-19 severities.

Narrative review: respiratory tract microbiome and never smoking lung cancer.

The lung microbiome was previously thought to be a sterile environment where only gaseous exchange takes place, but recent studies have shown the presence of microbiota in the lung. This review investigates the current literature on the effects of an environmental driven dysbiosis on the healthy oral and respiratory microbiome and its relationship to lung cancer risk in never-smokers. An online electronic search was performed on PubMed of all English-language literature using combinations of the following keywords: "lung cancer", "dysbiosis", "non-smokers", "oral microbiome", and "respiratory microbiome". All population-based studies reporting results on oral and/or respiratory microbiome in adults were considered for our narrative review. Metagenomic analyses have been performed on isolated samples from healthy participants and compared to samples from those with lung cancer. Research shows that a decrease in alpha diversity of microbes in the oral microbiome is associated with increased risk of lung cancer, along with differences in beta diversity in the sputum of lung cancer cases and healthy controls. Further, several studies have observed that significant changes in the abundance of genera such as increased abundance of Lactobacillales, Bacilli, and Firmicutes associated with an increased lung cancer risk among participants with exposure to certain household solid fuels. These findings suggest potential carcinogenic processes such as increased inflammation associated with changes in flora. Additionally, studies showed that increase in certain taxa such as Bacteroides and Spirochetes might have a protective effect on lung cancer risk. The review also provides insight into how understanding the microbial changes can be beneficial for lung cancer treatment and disease-free survival. Larger studies in different populations need to be performed to strengthen the current associations between microbial diversity and lung cancer risk.

Gut microbiota disorder induces liver dysfunction in polycystic ovary syndrome rats' model by regulating metabolite rosmarinic acid

AimsThe present study aims to investigate the impact of the gut microbiota and serum metabolites on the regulation of liver dysfunction in PCOS. Materials and methodsPCOS rat models were established by treating Sprague Dawley (SD) rats with DHEA (an androgen, 60 mg/kg) and LET (a nonsteroidal aromatase inhibitor, 1 mg/kg) for 90 days. Hematoxylin and eosin staining (H&E), Western blotting, and radioimmunoassay were employed to test ovarian and liver functions. Gut microbiome and serum metabolites were assessed using 16S rRNA amplicon sequencing and non-targeted metabolomics, respectively. The association between gut microbiota and serum metabolites was examined using Spearman analysis. Finally, using HepG2 cells to investigate the function of the serum metabolite rosmarinic acid (RA). Key findingsBoth Dehydroepiandrosterone (DHEA) and letrozole (LET) treatments induced a PCOS phenotype and liver dysfunction. However, LET resulted in more severe lipid accumulation and liver cell apoptosis than DHEA. 16S rRNA sequencing and non-targeted metabolomics analysis revealed significant differences in beta diversity and serum metabolite profiles among the three groups. Furthermore, among the significantly changed metabolites, RA was found to have a significant correlation with the levels of serum aspartate transaminase (AST) and lactate dehydrogenase (LDH) and could promote HepG2 cell apoptosis. SignificanceRestoring gut microbiota, altering serum metabolites and/or decreasing RA may provide a new insight to treat this complication.

Oral and Gut Microbiota Dysbiosis is Associated with Mucositis Severity in Autologous Hematopoietic Stem Cell Transplantation: Evidence from an Asian Population

Mucositis is a debilitating complication of hematopoietic stem cell transplant (HSCT). It is unclear how changes in the composition of microbiota, which are modulated by geographical location and ethnicity, may influence immune regulation leading to the development of mucositis, and the study of both oral and gut microbiota in a single population of autologous HSCT in the Asian region is lacking. The study aimed to characterize the oral and gut microbiota changes, and the impact on both oral and lower gastrointestinal (GI) mucositis, with its associated temporal changes in a population of adult autologous HSCT. Autologous HSCT patients aged 18 years old and above were recruited from Hospital Ampang, Malaysia, between April 2019 to December 2020. Mucositis assessments were conducted daily, whilst blood, saliva and fecal samples were collected prior to conditioning regimen, on Day 0, Day+7 and 6-month post-transplant. Longitudinal differences in alpha and beta diversities were determined using Wilcoxon signed-rank test and Permutational Multivariate Analysis of Variance, respectively. Changes in relative abundances of bacteria across timepoint were assessed using the Microbiome Multivariate Analysis by Linear Models function. The combined longitudinal effects of clinical, inflammatory and microbiota variables on mucositis severity were measured using the generalized estimating equation. From the 96 patients analyzed, oral mucositis and diarrhea (representing lower GI mucositis) were reported at 58.3% and 95.8%, respectively. Alpha and beta diversities were significantly different between sample types (p<0.001) and across timepoints, with alpha diversity reaching statistical significance at Day 0 in fecal (p<0.001) and Day+7 in saliva samples (p<0.001). Diversities normalized to baseline by 6-month. Significant microbiota, clinical and immunological factors were associated with increasing mucositis grades. Increasing relative abundances of saliva Paludibacter, Leuconostoc and Proteus, were associated with higher oral mucositis grades, whilst increasing relative abundances of fecal Rothia and Parabacteroides were associated with higher GI mucositis grades. Meanwhile, increasing relative abundances of saliva Lactococcus and Acidaminococcus, and fecal Bifidobacterium were associated with protective effects against worsening oral and GI mucositis grades, respectively. This study provides real-world evidence and insights into the dysbiosis of the microbiota in patients exposed to conditioning regimen during HSCT. Independent of clinical and immunological factors, we demonstrated significant associations between relative bacteria abundances with the increasing severities of oral and lower GI mucositis. The findings presented in our study offer a potential rationale to consider the inclusion of preventive and restorative measures targeting oral and lower GI dysbiosis as interventional strategies to ameliorate mucositis outcome in HSCT patients.

Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans

Fibre-based dietary interventions are at the forefront of gut microbiome modulation research, with a wealth of 16S rRNA information to demonstrate the prebiotic effects of isolated fibres. However, there is a distinct lack of data relating to the effect of a combination of soluble and insoluble fibres in a convenient-to-consume fruit juice food matrix on gut microbiota structure, diversity, and function. Here, we aimed to determine the impact of the MOJU Prebiotic Shot, an apple, lemon, ginger, and raspberry fruit juice drink blend containing chicory inulin, baobab, golden kiwi, and green banana powders, on gut microbiota structure and function. Healthy adults (n = 20) were included in a randomised, double-blind, placebo-controlled, cross-over study, receiving 60 mL MOJU Prebiotic Shot or placebo (without the fibre mix) for 3 weeks with a 3-week washout period between interventions. Shotgun metagenomics revealed significant between-group differences in alpha and beta diversity. In addition, the relative abundance of the phyla Actinobacteria and Desulfobacteria was significantly increased as a result of the prebiotic intervention. Nine species were observed to be differentially abundant (uncorrected p-value of &lt;0.05) as a result of the prebiotic treatment. Of these, Bifidobacterium adolescentis and CAG-81 sp900066785 (Lachnospiraceae) were present at increased abundance relative to baseline. Additionally, KEGG analysis showed an increased abundance in pathways associated with arginine biosynthesis and phenylacetate degradation during the prebiotic treatment. Our results show the effects of the daily consumption of 60 mL MOJU Prebiotic Shot for 3 weeks and provide insight into the functional potential of B. adolescentis.

O-262 The vaginal and faecal microbiome in women with recurrent pregnancy loss (RPL) before pregnancy according to the reproductive outcome after referral

Abstract Study question Is the vaginal or faecal microbiome different between primary RPL (pRPL) and secondary RPL (sRPL) patients, and is it related to reproductive outcome after referral? Summary answer Before pregnancy, the vaginal microbiome differed between pRPL and sRPL, and the faecal microbiome was altered in those who did not achieve pregnancy after follow-up. What is known already RPL is a heterogeneous condition leaving 50% of the couples without any known risk factors after the initial diagnostic workup. The microbiome of the reproductive tract seems to be an essential factor in women’s health, including pregnancy loss. Only a few studies have investigated the vaginal microbiome in women with RPL and found dysbiosis with a decrease in Lactobacillus crispatus. To our knowledge, the faecal microbiome in women with RPL has never been investigated. Study design, size, duration A prospective cohort study including 106 women referred with unexplained RPL between 04/2018 and 12/2019. Patients were routinely screened for established risk factors as recommended in the ESHRE RPL guideline. Exclusion criteria were &amp;gt;40 years, &amp;gt;1 shared child, the use of antibiotics, antimycotics and antiviral medication within the past two weeks, known chromosomal aberrations and major uterine malformations. Follow-up ranged between 12-31 months. Participants/materials, setting, methods The women were referred with a minimum of three unexplained consecutive pregnancy losses (64 pRPL and 42 sRPL) to the tertiary Recurrent Pregnancy Loss Unit at Copenhagen University Hospital (Rigshospitalet and Hvidovre Hospital), Denmark. Vaginal and faecal samples were collected before pregnancy and shot-gun sequenced on a DNBSEQ-G400 sequencer (MGI) using the high-throughput sequencing set (PE150 1000016952; MGI). Main results and the role of chance The beta diversity in the vaginal samples was significantly different (p = 0.001) between pRPL and sRPL, with Lactobacillus crispatus dominating more women with pRPL compared to sRPL who were dominated by Lactobacillus iners. Overall, twenty-nine patients (27.3% of the cohort) had vaginal dysbiosis defined as &amp;lt; 60% Lactobacillus spp. with no significant difference between pRPL and sRPL (vaginal dysbiosis in 21.8% vs. 35.7%, p = 0.118). During follow-up, 93 (87.7%) patients achieved pregnancy of which 50 (53.8%) resulted in a live birth and 43 (46.2%) in another pregnancy loss. There were no differences in age, BMI, alpha or beta diversity in the vaginal samples between the live birth group and pregnancy loss group. In the live birth group, 11 patients (22.0%) had vaginal dysbiosis compared with 32.1% of the rest of the cohort, p = 0.242. Ninety-three of 106 women collected a faecal sample at home after the first consultation and there was a significant difference in both alpha diversity (p = 0.014), beta diversity (p = 0.05) and richness (p = 0.001) between women who achieved pregnancy compared with those who did not conceive after follow-up. Limitations, reasons for caution Patients with recurrent pregnancy loss constitute a heterogenic population, which underlines the importance of subgroup comparisons such as pRPL and sRPL. Wider implications of the findings These findings underline the role of an altered vaginal and faecal microbiome as a potential risk factor for RPL. In-depth knowledge about the altered microbiome compositions in these patients can contribute to the generation of future treatment strategies and potentially improve patient care. Trial registration number not applicable

Modifications of lung microbiota structure in traumatic brain injury ventilated patients according to time and enteral feeding formulas: a prospective randomized study

BackgroundSpecialized diets enriched with immune nutrients could be an important supplement in patients (pts) with acute traumatic brain injury (TBI). Omega-3 and arginine may interact with immune response and microbiota. No data are available about the role of the specialized diets in modulating the lung microbiota, and little is known about the influence of lung microbiota structure in development of ventilator-associated pneumonia (VAP) in TBI pts. The aims of this study are to evaluate the impact of specific nutrients on the lung microbiota and the variation of lung microbiota in TBI pts developing VAP.MethodsA cohort of 31 TBI pts requiring mechanical ventilation in ICU was randomized for treatment with specialized (16pts) or standard nutrition (15pts). Alpha and beta diversity of lung microbiota were analyzed from bronco Alveolar Lavage (BAL) samples collected at admission and 7 days post-ICU admission in both groups. A further analysis was carried out on the same samples retrospectively grouped in VAP or no VAP pts.ResultsNone developed VAP in the first week. Thereafter, ten out of thirty-one pts developed VAP. The BAL microbiota on VAP group showed significant differences in beta diversity and Staphylococcus and Acinetobacter Genera were high. The specialized nutrition had influence on beta diversity that reached statistical significance only in Bray–Curtis distance.ConclusionOur data suggest that TBI patients who developed VAP during ICU stay have different structures of BAL microbiota either at admission and at 7 days post-ICU admission, while no correlation has been observed between different enteral formulas and microbiota composition in terms of richness and evenness. These findings suggest that targeting the lung microbiota may be a promising approach for preventing infections in critically ill patients.

Avian biodiversity assessment studies in a Neotropical wetland – the combination of sampling methods makes the difference

In studies of avian diversity, many different methods have been applied. Since methodological approaches may affect research results, the choice of a given methodology must be consistent with the scientific objectives. The aim of this study was to investigate how different methodologies with their intrinsic limitations help detect and monitor birds to evaluate how they complement each other in the survey of species. Three different assessment methods, mist nets, point counts, and autonomous acoustic recordings were used to serve this purpose in a study of different Pantanal habitats, such as savannas and forests. The point counts detected more species (126 species) than the two other methods autonomous acoustic recordings (113 species) and mist nets (79 species). We observed significant differences in the number of species detected by mist nets and the other two methods. Each survey method identified exclusive species. When comparing habitats, all three methods showed significant differences in bird species composition. Savannas were richer in bird species than forests, and replacement was the main driver responsible for the differences in beta diversity between the habitats. The three methodologies, when applied together, proved to be complementary in avian species detection.

Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis.

Coral diseases are one of the leading causes of declines in coral populations. In the Caribbean, white band disease (WBD) has led to a substantial loss of Acropora corals. Although the etiologies of this disease have not been well described, characterizing the coral microbiome during the transition from a healthy to diseased state is critical for understanding disease progression. Coral nurseries provide unique opportunities to further understand the microbial changes associated with diseased and healthy corals, because corals are monitored over time. We characterized the microbiomes before and during an outbreak of WBD in Acropora cervicornis reared in an ocean nursery in Little Cayman, CI. We asked (1) do healthy corals show the same microbiome over time (before and during a disease outbreak) and (2) are there disease signatures on both lesioned and apparently healthy tissues on diseased coral colonies? Microbial mucus-tissue slurries were collected from healthy coral colonies in 2017 (before the disease) and 2019 (during the disease onset). Diseased colonies were sampled at two separate locations on an individual coral colony: at the interface of Disease and ∼10 cm away on Apparently Healthy coral tissue. We sequenced the V4 region of the 16S rRNA gene to characterize bacterial and archaeal community composition in nursery-reared A. cervicornis. We assessed alpha diversity, beta diversity, and compositional differences to determine differences in microbial assemblages across health states (2019) and healthy corals between years (2017 and 2019). Microbial communities from healthy A. cervicornis from 2017 (before disease) and 2019 (after disease) did not differ significantly. Additionally, microbial communities from Apparently Healthy samples on an otherwise diseased coral colony were more similar to Healthy colonies than to the diseased portion on the same colony for both alpha diversity and community composition. Microbial communities from Diseased tissues had significantly higher alpha diversity than both Healthy and Apparently Healthy tissues but showed no significant difference in beta-diversity dispersion. Our results show that at the population scale, Healthy and Apparently Healthy coral tissues are distinct from microbial communities associated with Diseased tissues. Furthermore, our results suggest stability in Little Cayman nursery coral microbiomes over time. We show healthy Caymanian nursery corals had a stable microbiome over a two-year period, an important benchmark for evaluating coral health via their microbiome.

1143-P: Elevated Serum IgA and the Gut Microbiome in Pediatric Type 1 Diabetes (T1D)

Elevated serum IgA occurs in ~20% of children with new onset T1D, although its potential role in T1D pathogenesis is not understood. Gut dysbiosis is present at onset of T1D and is strongly associated with its pathogenesis. Mucosal IgA is well known to influence the microbiome and vice versa. In animal models, serum IgA responds to microbiome changes, thereby inducing a protective response to gut invasion by pathogens. However, the relationship between gut microbiome and serum IgA in humans with T1D is unknown. Thus, we aimed to assess if elevated serum IgA is associated with gut dysbiosis at T1D onset. We enrolled 47 children between 7/2021 and 9/2022: New onset T1D with elevated serum IgA (T1D-Hi-IgA, n=14), new onset T1D with normal serum IgA (T1D-Nl-IgA, n=18) and controls (siblings of new onset T1D, n=15). Exclusions: &amp;lt;2 yrs age; antibiotics; probiotics; inflammatory bowel disease; celiac disease; or acute illness &amp;lt;10 days of stool collection. Demographic and clinical variables, diet questionnaires and stool were collected. Stool microbiome was determined via 16Sv4 rDNA sequencing. Differences in alpha and beta diversity along with taxa abundance were assessed. We found that the relative abundance of members of families Oscillospiraceae and Lachnospiraceae, both of which contain butyrate producers, were significantly associated with elevated IgA irrespective of T1D status (p&amp;lt;0.05); higher in T1D-Hi-IgA vs T1D-Nl-IgA (p&amp;lt;0.05); yet similar in T1D-Hi-IgA vs controls. Measures of alpha diversity, including richness and evenness, were also increased in T1D-Hi-IgA vs T1D-Nl-IgA, though these differences did not reach significance (richness: p=0.074; evenness: p=0.135). Similar results were observed for beta diversity. In sum, in children with new onset T1D, elevated serum IgA is associated with beneficial microbial taxa such as butyrate producers, with a trend towards increased diversity, similar to healthy siblings. Further studies are needed to understand its involvement in T1D pathogenesis. Disclosure A.Thakkar: None. M.J.Redondo: None. J.Hajjar: None. J.Petrosino: None. K.L.Hoffman: Consultant; Cooper Surgical. J.Cormier: None. M.Ahmed: None. X.C.Huang: None.

IgA-Biome Profiles Correlate with Clinical Parkinson's Disease Subtypes.

Parkinson's disease is a heterogeneous neurodegenerative disorder with distinctive gut microbiome patterns suggesting that interventions targeting the gut microbiota may prevent, slow, or reverse disease progression and severity. Because secretory IgA (SIgA) plays a key role in shaping the gut microbiota, characterization of the IgA-Biome of individuals classified into either the akinetic rigid (AR) or tremor dominant (TD) Parkinson's disease clinical subtypes was used to further define taxa unique to these distinct clinical phenotypes. Flow cytometry was used to separate IgA-coated and -uncoated bacteria from stool samples obtained from AR and TD patients followed by amplification and sequencing of the V4 region of the 16 S rDNA gene on the MiSeq platform (Illumina). IgA-Biome analyses identified significant alpha and beta diversity differences between the Parkinson's disease phenotypes and the Firmicutes/Bacteroides ratio was significantly higher in those with TD compared to those with AR. In addition, discriminant taxa analyses identified a more pro-inflammatory bacterial profile in the IgA+ fraction of those with the AR clinical subclass compared to IgA-Biome analyses of those with the TD subclass and with the taxa identified in the unsorted control samples. IgA-Biome analyses underscores the importance of the host immune response in shaping the gut microbiome potentially affecting disease progression and presentation. In the present study, IgA-Biome analysis identified unique proinflammatory microbial signature in the IgA+ fraction of those with AR that would have otherwise been undetected using conventional microbiome analysis approaches.

The oral microbiome of implant-abutment screw holes compared with the peri-implant sulcus and natural supragingival plaque in healthy individuals.

An implant-supported prosthesis consists of an implant fixture, an abutment, an internal screw that connects the abutment to the implant fixture, and the upper prosthesis. Numerous studies have investigated the microorganisms present on the implant surface, surrounding tissues, and the subgingival microflora associated with peri-implantitis. However, there is limited information regarding the microbiome within the internal screw space. In this study, microbial samples were collected from the supragingival surfaces of natural teeth, the peri-implant sulcus, and the implant-abutment screw hole, in order to characterize the microbiome of the internal screw space in healthy subjects. Samples were obtained from the supragingival region of natural teeth, the peri-implant sulcus, and the implant screw hole in 20 healthy subjects. DNA was extracted, and the V3-V4 region of the 16S ribosomal RNA was sequenced for microbiome analysis. Alpha diversity, beta diversity, linear discriminant analysis effect size (LEfSe), and network analysis were employed to compare the characteristics of the microbiomes. We observed significant differences in beta diversity among the samples. Upon analyzing the significant taxa using LEfSe, the microbial composition of the implant-abutment screw hole's microbiome was found to be similar to that of the other sampling sites' microbiomes. Moreover, the microbiome network analysis revealed a unique network complexity in samples obtained from the implant screw hole compared to those from the other sampling sites. The bacterial composition of the biofilm collected from the implant-abutment screw hole exhibited significant differences compared to the supra-structure of the implant. Therefore, long-term monitoring and management of not only the peri-implant tissue but also the implant screw are necessary.

Mapping the vaginal microbiota variations in women from a community clinic in Mumbai, India

PurposeThe vaginal microbiome contributes significantly to women’s reproductive health and fluctuates due to various physiological and pathological factors. The study’s objective is to map the vaginal microbiome of non-pregnant women and evaluate variations based on various potential factors influencing vaginal milieu. MethodsFifty-two sexually active, non-pregnant women between 18 and 45 years were recruited from a community clinic and clinical history was recorded. Vaginal swabs were collected to assess the vaginal microbiome by sequencing the V3-V4 region of the 16S rRNA using the Illumina HiSeq platform, followed by data analysis with QIIME 2. Vaginal milieu was assessed by Nugent score and profiling cytokines in the cervico-vaginal lavage. ResultsLactobacillus iners (34.3%) were the most abundant species in all women. Significant changes in abundance of genera (Lactobacillus, Prevotella and Anaerococcus), expression of pro-inflammatory cytokine IFN-γ and changes in alpha and beta diversity was observed in women having asymptomatic bacterial vaginosis (BV). Differences in beta diversity were seen between healthy women and women exhibiting presence of Candida spp. Variations in the abundance of genera (Lactobacillus, Bifidobacterium, Porphyromonas) were observed in women who had delivery less than twelve months back, probably as more of these women (50%, 53.7%) had higher abnormal Nugent score. ConclusionLactobacillus iners was the most prevalent vaginal species in women from a Mumbai community clinic. Maximum variations in the vaginal microbiome characterized by a perturbation of the Lactobacillus predominant vaginal microbiota are seen in those women who have asymptomatic BV and childbirth within last twelve months.

Legacy effects of intensified drought on the soil microbiome in a mesic grassland

AbstractThe soil microbiome response to global change drivers remains largely unclassified, with current studies showing contrasting results to several global change drivers. One such driver, drought, is increasing in severity and frequency due to climate change. Further, legacy effects, or long‐lasting impacts after drought has subsided, could have lasting impacts on the soil microbiome with important consequences for ecosystem functioning. Thus, our study aimed to understand how the soil microbiome responds after a severe, prolonged drought and whether legacy effects persist post‐drought. We measured soil microbial community response in a mesic grassland for two years after a four‐year experimental drought in a native tallgrass prairie. The experimental drought was imposed either (1) chronically by reducing each growing season rainfall event by 66% or (2) intensely by completely eliminating growing season rainfall until an ~45% reduction in mean annual rainfall (climatic average) was achieved. The bacterial community showed no legacies in the first season post‐drought in response to either chronic or intense drought but showed an increased abundance of Verrucomicrobia and decreased richness in both treatments in the second growing season after the drought treatments ended. In the first and second post‐drought growing seasons, we found small differences in beta diversity between the control and intense drought treatment for fungal communities but not for the chronic drought treatment. Further, we found that the two main phyla of fungi, Ascomycota and Basidiomycota, showed reduced relative abundance post‐drought in the intense drought treatment. Overall, few legacies in soil microbial communities persisted after a four‐year experimentally induced drought. However, our results show that the nature of the drought—chronic versus intense—can differentially impact fungal versus bacterial short‐term legacies. These results suggest that the soil microbiome is for the most part drought resistant (responds little during drought) and/or resilient (quickly recovers post‐drought, since a study at the same site found that drought impacted the bacterial community) in this mesic grassland.

Drivers of the spatiotemporal patterns of the mangrove crab metacommunity in a tropical bay.

Revealing community patterns and driving forces is essential in community ecology and a prerequisite for effective management and conservation efforts. However, the mangrove ecosystem and its important fauna group such as the crabs, still lack multi-processes research under metacommunity framework, resulting in evidence and theorical application gaps. To fill these gaps, we selected China's most representative mangrove bay reserve in tropical zone as a stable experimental system and conducted a seasonal investigation (July 2020, October 2020, January 2021, and April 2021) of mangrove crabs. We performed a multi-approach analysis using both pattern-based and mechanistic method to distinguish the processes driving the mangrove crab metacommunity. Our results showed that the crab metacommunity exhibits a Clementsian pattern in the bay-wide mangrove ecosystem but is influenced by both local environmental heterogeneity and spatial processes, thus representing a combined paradigm of species sorting and mass effect. Moreover, the long-distance spatial constraints are more pronounced compared to the local environmental factors. This is reflected in the greater importance of the broad-scale Moran's Eigenvector Maps, the distance-decay pattern of similarity, and the difference in beta diversity dominated by the turnover component. This pattern changes throughout the year, mainly due to changes in dominant functional groups caused by the stress of changes in water salinity and temperature induced by air temperature and precipitation. This research provides multi-dimension research data and relevant analysis, offering clear evidence for understanding the patterns and related driving forces of crab metacommunity in tropical bay mangroves, and verifies the applicability of some general laws in the system. Future studies can address more diverse spatiotemporal scales, gaining a clearer understanding to serve the conservation of mangrove ecosystems and economically important fishery species.

The effect of the formalin-fixed paraffin-embedded process on salivary microbiota profiling.

In recent years, bacterial DNA in formalin-fixed paraffin-embedded (FFPE) samples has been recognized as a valuable bioresource for microbiota studies. This study aimed to examine the effect of the FFPE process on microbiota profiling to evaluate whether FFPE samples could serve as an alternative bioresource to fresh samples in oral microbiota studies. Fresh saliva was collected from nine subjects. The pellets obtained by centrifuging the collected saliva were fixed in formalin, then dehydrated and embedded in paraffin to prepare FFPE samples. The abundance of the hypervariable regions V1-9, V1-2, and V3-4 of the 16S rRNA gene in fresh and FFPE samples was relatively compared. In addition, microbiota profiling was performed to compare the results between the two sample types. The results showed that the FFPE process resulted in a certain degree of fragmentation of the 16S rRNA gene. However, the V1-2 region was relatively well-preserved compared to the V1-9 and V3-4 regions, suggesting that short regions are suitable targets for oral microbiota analysis. Importantly, there were no significant differences in alpha and beta diversity of microbiota between fresh and FFPE samples, and microbiota profiles were similar between the two sample types, suggesting that FFPE samples could be a valuable bioresource for oral microbiota studies.

Altered gut microbiota in older adults with mild cognitive impairment: a case-control study.

The microbiota-gut-brain axis is implicated in Alzheimer's disease. Gut microbiota alterations in mild cognitive impairment (MCI) are inconsistent and remain to be understood. This study aims to investigate the gut microbial composition associated with MCI, cognitive functions, and structural brain differences. A nested case-control study was conducted in a community-based prospective cohort where detailed cognitive functions and structural brain images were collected. Thirty-one individuals with MCI were matched to sixty-five cognitively normal controls by age strata, gender, and urban/rural area. Fecal samples were examined using 16S ribosomal RNA (rRNA) V3-V4 sequencing. Compositional differences between the two groups were identified and correlated with the cognitive functions and volumes/thickness of brain structures. There was no significant difference in alpha and beta diversity between MCIs and cognitively normal older adults. However, the abundance of the genus Ruminococcus, Butyricimonas, and Oxalobacter decreased in MCI patients, while an increased abundance of nine other genera, such as Flavonifractor, were found in MCIs. Altered genera discriminated MCI patients well from controls (AUC = 84.0%) and were associated with attention and executive function. This study provides insights into the role of gut microbiota in the neurodegenerative process.