Bacterial Relative Abundance Research Articles

466-P: Changes in Oral and Intestinal Bacterial Flora Associated with Pain Thresholds

Small fiber neuropathy (SFN) manifests from the early stages of diabetic polyneuropathy. Changes in the oral and intestinal bacterial flora are known to be associated with the onset and progression of diabetes and its complications. However, correlation between SFN and each bacterial flora has not yet been investigated. In the 2018 Iwaki health promotion project, which is a local health promotion study in Aomori prefecture, 1037 participants (431 males and 6females including 814 non-glucose metabolism disorders, 143 fasting hyperglycemia (IFG) , and 80 type 2 diabetic cases (DM) , were evaluated. SFN was evaluated by the pain threshold evoked by intraepidermal electrical stimulation (PINT) . A PINT value of 0.or less was designated as Pint-L, and otherwise was designated as Pint-H. DNA was isolated from saliva and feces and relative bacterial abundance was determined with a next-generation sequencer. Bacteria that account for 1% or more of all bacteria were examined. PINT was significantly increased in IFG (0.12 ± 0.11mA) and DM (0.15 ± 0.13mA) compared to healthy subjects (0.± 0.08mA) (p<0.vs. IFG, p <0.vs. DM) . No significant difference was found depending on the PINT value in the bacteria flora of oral cavity. There were significant differences of gut bacterial flor in α and β-diversity (p<0.05) and principal component analysis (p <0.01) depending on the PINT value. The genus Bacteroides was significantly higher in PINT-H than in PINT-L (p<0.01) . After IFG and DM cases were excluded, a significant difference was maintained. The amount of bacteroides was significantly correlated with age, abdominal circumference, fasting blood glucose, HbA1c (p<0.001) , BMI and PINT value (p <0.05) . In the multiple regression analysis adjusted for these factors, PINT was significantly correlated with the amount of Bacteroides (β = -0.089, p = 0.026) . Our results suggest that the gut Bacteroides may correlate with SFN. The involvement of deterioration of glucose metabolism may not be high in this correlation. Disclosure K.Kudoh: None. Y.Takeuchi: None. S.Osonoi: None. T.Sasaki: None. S.Ogasawara: None. S.Yagihashi: None. H.Mizukami: None.

A Deep Look at the Vaginal Environment During Pregnancy and Puerperium.

A deep comprehension of the vaginal ecosystem may hold promise for unraveling the pathophysiology of pregnancy and may provide novel biomarkers to identify subjects at risk of maternal-fetal complications. In this prospective study, we assessed the characteristics of the vaginal environment in a cohort of pregnant women throughout their different gestational ages and puerperium. Both the vaginal bacterial composition and the vaginal metabolic profiles were analyzed. A total of 63 Caucasian women with a successful pregnancy and 9 subjects who had a first trimester miscarriage were enrolled. For the study, obstetric examinations were scheduled along the three trimester phases (9-13, 20-24, 32-34 gestation weeks) and puerperium (40-55 days after delivery). Two vaginal swabs were collected at each time point, to assess the vaginal microbiome profiling (by Nugent score and 16S rRNA gene sequencing) and the vaginal metabolic composition (1H-NMR spectroscopy). During pregnancy, the vaginal microbiome underwent marked changes, with a significant decrease in overall diversity, and increased stability. Over time, we found a significant increase of Lactobacillus and a decrease of several genera related to bacterial vaginosis (BV), such as Prevotella, Atopobium and Sneathia. It is worth noting that the levels of Bifidobacterium spp. tended to decrease at the end of pregnancy. At the puerperium, a significantly lower content of Lactobacillus and higher levels of Gardnerella, Prevotella, Atopobium, and Streptococcus were observed. Women receiving an intrapartum antibiotic prophylaxis for Group B Streptococcus (GBS) were characterized by a vaginal abundance of Prevotella compared to untreated women. Analysis of bacterial relative abundances highlighted an increased abundance of Fusobacterium in women suffering a first trimester abortion, at all taxonomic levels. Lactobacillus abundance was strongly correlated with higher levels of lactate, sarcosine, and many amino acids (i.e., isoleucine, leucine, phenylalanine, valine, threonine, tryptophan). Conversely, BV-associated genera, such as Gardnerella, Atopobium, and Sneathia, were related to amines (e.g., putrescine, methylamine), formate, acetate, alcohols, and short-chain fatty-acids (i.e., butyrate, propionate).

Effects of dietary bacitracin or Bacillus subtilis on the woody breast myopathy-associated gut microbiome of Eimeria spp. challenged and unchallenged broilers

Study suggested that dysbiosis of the gut microbiota may affect the etiology of woody breast (WB). In the current study, the cecal microbiota and WB in chickens fed three different diets were investigated. A total of 504 male chicks were used in a randomized complete block design with a 3 (Diet) × 2 (Challenge) factorial arrangement of treatments with 6 replicates per treatment, 6 treatments per block, and 14 birds per treatment. The experimental diets were a control diet (corn-soybean meal basal diet), an antibiotic diet (basal diet + 6.075 mg bacitracin/kg feed), and a probiotic diet (basal diet + 2.2 × 108 CFU Bacillus subtilis PB6/kg feed). On d 14, birds that were assigned to the challenge treatment received a 20 × live cocci vaccine. On d 41, breast muscle hardness in live birds was palpated and grouped into normal (NB) and WB phenotypes. Cecal contents were collected and their bacterial compositions were analyzed and compared. The genomic DNA of the cecal contents was extracted and the V3 and V4 regions of 16S rRNA gene were amplified and sequenced via an Illumina MiSeq platform. There were no differences (P > 0.05) in Shannon and Chao 1 indexes between the challenges, diets, and phenotypes (NB vs. WB). However, there was a difference (P = 0.001) in the beta diversity of the samples between the challenged and nonchallenged groups. Relative bacterial abundance differed (false discovery rate, FDR < 0.05) between the challenge treatments, but there were no significant differences (FDR > 0.05) among the three diets or two phenotypes. Predicted energy metabolism, nucleotide metabolism, and amino acid and coenzyme biosynthesis activities only differed (q-value < 0.05) between challenged and nonchallenged groups. The cocci challenge altered the gut microbial composition on Butyricicoccus pullicaecorum, Sporobacter termitidis, and Subdoligranulum variabile, but the dietary antibiotic and probiotic treatments did not impact gut microbial composition. No strong association was found between WB myopathy and gut microbial composition in this study.

Impact of Food-Based Weight Loss Interventions on Gut Microbiome in Individuals with Obesity: A Systematic Review.

The observation that the gut microbiota is different in healthy weight as compared with the obese state has sparked interest in the possible modulation of the microbiota in response to weight change. This systematic review investigates the effect of food-based weight loss diets on microbiota outcomes (α-diversity, β-diversity, relative bacterial abundance, and faecal short-chain fatty acids, SCFAs) in individuals without medical comorbidities who have successfully lost weight. Nineteen studies were included using the keywords ‘obesity’, ‘weight loss’, ‘microbiota’, and related terms. Across all 28 diet intervention arms, there were minimal changes in α- and β-diversity and faecal SCFA concentrations following weight loss. Changes in relative bacterial abundance at the phylum and genus level were inconsistent across studies. Further research with larger sample sizes, detailed dietary reporting, and consistent microbiota analysis techniques are needed to further our understanding of the effect of diet-induced weight loss on the gut microbiota.

Impacts of nano-titanium dioxide toward Vallisneria natans and epiphytic microbes

In this study, Vallisneria natans plants were exposed to 5 and 20 nm of titanium dioxide nanoparticles (TiO₂ NPs) anatase and 600–1000 nm of bulk at 5 and 20 mg/L for 30 days. SEM images and EDX spectra revealed that epiphytic biofilms were more prone to TiO₂ NPs adhesion than bare plant leaves. TiO₂ NPs injured plant leaf cells, ruptured epiphytic diatoms membranes and increased the ratio of free-living microbes. The TN, NH4⁺-N and NO3ˉ-N concentrations significantly decreased, respectively, by 44.9%, 33.6%, and 23.6% compared to bulk treatments after 30 days due to macrophyte damage and a decline in diversity of epiphytic bacterial community and abundance of nitrogen cycle bacteria. TiO₂ NPs size-dependent decrease in bacterial relative abundance was detected, including phylum Cyanobacteria, Planctomycetes, and Verrucomicrobia. Although TiO₂ NPs increased eukaryotic diversity and abundance, abundances of Bacillariophyceae and Vampyrellidae classes and Gastrotricha and Phragmoplastophyta phylum decreased significantly under TiO₂ NPs exposure compared to bulk and control. TiO₂ NPs reduced intensities of interaction relationships among epiphytic microbial genera. This study shed new light on the potential effects of TiO₂ NPs toxicity toward aquatic plants and epiphytic microbial communities and its impacts on nitrogen species removal in wetlands.

Changes to Gut Microbiota Following Systemic Antibiotic Administration in Infants.

Long-term antibiotic use can have consequences on systemic diseases, such as obesity, allergy, and depression, implicating the causal role of gut microbiome imbalance. However, the evaluation of the effect of antibiotics in early infancy on alterations to the gut microbiome remains poorly understood. This study aimed to evaluate the gut microbiome state in infancy following systemic antibiotic treatment. Twenty infants under 3 months of age who had received antibiotics for at least 3 days were enrolled, and their fecal samples were collected 4 weeks after antibiotic administration finished. Thirty-four age-matched healthy controls without prior exposure to antibiotics were also assessed. The relative bacterial abundance in feces was obtained via sequencing of 16 S rRNA genes, and alpha and beta diversities were evaluated. At the genus level, the relative abundance of Escherichia/Shigella and Bifidobacterium increased (p = 0.03 and p = 0.017, respectively) but that of Bacteroides decreased (p = 0.02) in the antibiotic treatment group. The microbiome of the antibiotic treatment group exhibited an alpha diversity lower than that of the control group. Thus, systemic antibiotic administration in early infancy affects the gut microbiome composition even after a month has passed; long-term studies are needed to further evaluate this.

Cropping practices manipulate soil bacterial structure and functions on the Qinghai–Tibet Plateau

There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai–Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae–legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae–legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai–Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.

Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses.

ABSTRACTThe success of tropical scleractinian corals depends on their ability to establish symbioses with microbial partners. Host phylogeny and traits are known to shape the coral microbiome, but to what extent they affect its composition remains unclear. Here, by using 12 coral species representing the complex and robust clades, we explored the influence of host phylogeny, skeletal architecture, and reproductive mode on the microbiome composition, and further investigated the structure of the tissue and skeleton bacterial communities. Our results show that host phylogeny and traits explained 14% of the tissue and 13% of the skeletal microbiome composition, providing evidence that these predictors contributed to shaping the holobiont in terms of presence and relative abundance of bacterial symbionts. Based on our data, we conclude that host phylogeny affects the presence of specific microbial lineages, reproductive mode predictably influences the microbiome composition, and skeletal architecture works like a filter that affects bacterial relative abundance. We show that the β-diversity of coral tissue and skeleton microbiomes differed, but we found that a large overlapping fraction of bacterial sequences were recovered from both anatomical compartments, supporting the hypothesis that the skeleton can function as a microbial reservoir. Additionally, our analysis of the microbiome structure shows that 99.6% of tissue and 99.7% of skeletal amplicon sequence variants (ASVs) were not consistently present in at least 30% of the samples, suggesting that the coral tissue and skeleton are dominated by rare bacteria. Together, these results provide novel insights into the processes driving coral-bacterial symbioses, along with an improved understanding of the scleractinian microbiome.IMPORTANCE The rapid decline of coral reefs, driven by climate changes, calls for manipulative interventions such as the use of probiotics, which can assist the resilience of these ecosystems. However, many knowledge gaps still exist in our understanding of coral-bacterial symbioses that need to be addressed before effectively applying interventions like probiotics. Here, by investigating the microbiomes of 12 common coral species we show that the associations with bacterial symbionts, thought to be critical to coral health, were influenced to some extent by host phylogeny, skeletal architecture, reproduction, and anatomical compartments. We therefore propose that fundamental and applied functional exploration of coral-associated microbes will help inform successful reef management measures.

Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women.

BackgroundBacterial colonization and associations with bacterial vaginosis (BV) signs and symptoms (Amsel criteria) may vary between populations. We assessed relationships between vaginal bacteria and Amsel criteria among two populations.MethodsKenyan participants from the placebo arm of the Preventing Vaginal Infections (PVI) trial and participants from a Seattle-based cross-sectional BV study were included. Amsel criteria were recorded at study visits, and the vaginal microbiota was characterized using 16S rRNA gene sequencing. Logistic regression models, accounting for repeat visits as appropriate, were fit to evaluate associations between bacterial relative abundance and each Amsel criterion.ResultsAmong 84 PVI participants (496 observations) and 220 Seattle participants, the prevalence of amine odor was 25% and 40%, clue cells 16% and 37%, vaginal discharge 10% and 52%, elevated vaginal pH 69% and 67%, and BV 13% and 44%, respectively. BV-associated bacterium 1 (BVAB1) was positively associated with all Amsel criteria in both populations. Eggerthella type 1, Fannyhessea (Atopobium) vaginae, Gardnerella spp., Sneathia amnii, and Sneathia sanguinegens were positively associated with all Amsel criteria in the Seattle study, and all but discharge in the PVI trial.ConclusionsCore vaginal bacteria are consistently associated with BV signs and symptoms across two distinct populations of women.

Probiotic strategy for biofouling control through direct injection of quorum-quenching bacteria into membrane bioreactors

In membrane bioreactors (MBRs), N-acyl homoserine lactones (AHLs)-related quorum sensing (QS) has been described as one of the main causes of biofouling during wastewater treatment. Quorum-quenching (QQ) bacteria for the mitigation of QS in MBRs have been applied but limited to entrapping methods only. Thus, this study investigates the direct injection of different doses (0–77.2 mg/d) of unentrapped QQ strains (Rhodococcus sp. BH4) into a probiotic QQ MBR (i.e., bioaugmented reactor) while monitoring the changes in fouling rates as well as microbial communities, biopolymers, signal molecules, and treatment performances. The QQ bacteria show effective biofouling mitigation in diverse MBR phases, but a halt in QQ bacteria injection leads to increased fouling rates in the probiotic QQ MBR. The QQ bacteria exhibit a noticeable AHL degradation rate during BH4 inoculation as opposed to when inoculation is halted. They also have significant inhibitory effects on the generation of soluble carbohydrates and proteins. However, cell-bound extracellular polymeric substance (EPS) concentrations are relatively higher in the probiotic QQ reactor despite decreased fouling rates. This can be ascribed to the production of EPS by injected BH4, as revealed in pure BH4 batch cultures. Probiotic QQ has impacts on both the relative bacterial abundance and the overall microbial composition. Thiothrix is identified as the most dominant genus in the mixed liquor of both MBRs; however, its relative abundance becomes low in the probiotic MBR during QQ bacteria injection. These findings provide valuable information that will foster the development of improved QQ strategies in MBRs.

Understanding the mechanisms behind micro-aeration to enhance anaerobic digestion of corn straw

Micro-aeration has been shown to be favorable for anaerobic digestion (AD) process. However, the underlying mechanisms are not fully revealed. In this study, the effects of micro-aeration on AD process were investigated, the underlying mechanisms were also explored by comprehensively analysis of the substrate degradation, intermediate products, electron-transfer capacity, key enzymes and microbial communities. Results showed micro-aeration could benefit the AD process, and the beneficial effects were oxygen intensity-dependent. Maximum methane yield (262.0 ± 6.0 mL/(g·VS)) was achieved at micro-aeration of 0.2 mL/(g·VS·day), which was 7.8% higher than that of the control (without micro-aeration). The volatile fatty acids concentration, cellulase activity, soluble humic acids (SHAs) concentration and substrate degradation rate were all enhanced under micro-aeration condition. Moreover, micro-aeration could regulate the bacterial and archaeal communities: bacterial diversities and relative abundances of facultative and acetate-oxidizing bacteria (e.g., Firmicutes, Synergistota and Spirochaetota) increased, leading to higher substrate utilization rate; archaeal diversities decreased while oxygen-tolerating methanogens (e.g., Methanobacterium) became dominant to promote the methanogenesis. AD system with micro-aeration showed higher electron-transfer capacity and better conductive environment due to the increased SHAs concentration. The increased relative abundance of direct-interspecies-electron-transfer (DIET)-associated microbes could be favorable to DIET-based syntrophic methanogenesis which promotes AD under micro-aeration.

Changes in soil microbial community following the conversion of wasteland to cotton land in saline-sodic region of Northwest China

Soil microbes are essential drivers of nutrient transformation and energy flow; nevertheless, how the soil microbial communities in oasis agroecosystems respond to the conversion from wasteland to cropland remains unknown. This study selected six cotton fields that differed in the time since reclamation (0–23 years) in Xinjiang, Northwest China. Soil from the top 20 cm layer was sampled, and microbial communities were analyzed using high-throughput sequencing. We found significantly decreasing soil fungal and bacterial relative abundances during the initial nine years of conversion, which then increased before stabilizing 15–23 years post-conversion. Average abundances of fungal and bacterial taxa increased in all croplands compared with uncultivated wasteland, by 39.57% and 18.76%, respectively. Converting wasteland to cotton land significantly increased soil bacterial α-diversity (Chao1, Pielou's E, and Simpson indices) except in Good's coverage index. Increasing length of time since conversion shaped soil microbial community structure, with increases in the relative abundances of the fungal phylum Mortierellomycota and the bacterial phyla Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes; concurrent with decreases of the fungal phylum Ascomycota and the bacterial phyla Proteobacteria, Bacteroidetes, and Firmicutes. Our study reveals that short-term (9–13 years) conversion increases microbial richness and diversity due to the improvement of soil fertility; however, a longer time since conversion (15–23 years) might be detrimental to microbial community structure given the potential for secondary salinization.

Metagenomics Versus Metatranscriptomics of the Murine Gut Microbiome for Assessing Microbial Metabolism During Inflammation.

Shotgun metagenomics studies have improved our understanding of microbial population dynamics and have revealed significant contributions of microbes to gut homeostasis. They also allow in silico inference of the metagenome. While they link the microbiome with metabolic abnormalities associated with disease phenotypes, they do not capture microbial gene expression patterns that occur in response to the multitude of stimuli that constantly ambush the gut environment. Metatranscriptomics closes that gap, but its implementation is more expensive and tedious. We assessed the metabolic perturbations associated with gut inflammation using shotgun metagenomics and metatranscriptomics. Shotgun metagenomics detected changes in abundance of bacterial taxa known to be SCFA producers, which favors gut homeostasis. Bacteria in the phylum Firmicutes were found at decreased abundance, while those in phyla Bacteroidetes and Proteobacteria were found at increased abundance. Surprisingly, inferring the coding capacity of the microbiome from shotgun metagenomics data did not result in any statistically significant difference, suggesting functional redundancy in the microbiome or poor resolution of shotgun metagenomics data to profile bacterial pathways, especially when sequencing is not very deep. Obviously, the ability of metatranscriptomics libraries to detect transcripts expressed at basal (or simply low) levels is also dependent on sequencing depth. Nevertheless, metatranscriptomics informed about contrasting roles of bacteria during inflammation. Functions involved in nutrient transport, immune suppression and regulation of tissue damage were dramatically upregulated, perhaps contributed by homeostasis-promoting bacteria. Functions ostensibly increasing bacteria pathogenesis were also found upregulated, perhaps as a consequence of increased abundance of Proteobacteria. Bacterial protein synthesis appeared downregulated. In summary, shotgun metagenomics was useful to profile bacterial population composition and taxa relative abundance, but did not inform about differential gene content associated with inflammation. Metatranscriptomics was more robust for capturing bacterial metabolism in real time. Although both approaches are complementary, it is often not possible to apply them in parallel. We hope our data will help researchers to decide which approach is more appropriate for the study of different aspects of the microbiome.

Investigating Chemical and Biological Control Applications for Pythium Root Rot Prevention and Impacts on Creeping Bentgrass Putting Green Rhizosphere Bacterial Communities.

Pythium root rot (PRR) is a disease that can rapidly devastate large swaths of golf course putting greens, with little recourse once symptoms appear. Golf courses routinely apply preventive fungicides for root diseases, which may alter the rhizosphere microbiome, leading to unintended effects on plant health. A multiyear field trial was initiated on a 'T-1' creeping bentgrass (Agrostis stolonifera L. cultivar T-1) putting green in College Park, Maryland to evaluate preventive PRR management for disease suppression and effects on rhizosphere bacterial communities. Fungicides commonly used to prevent PRR and a biological fungicide were repeatedly applied to experimental plots throughout the growing season. Rhizosphere samples were collected twice annually from each plot for evaluation of rhizosphere bacterial communities through amplicon sequencing and monitoring of biological control organism populations via quantitative PCR. Cyazofamid was the only treatment to suppress PRR in both years compared with the control. Fosetyl-Al on a 14-day interval and Bacillus subtilis QST713 also reduced PRR severity in 2019 compared with the nontreated control. Treatments did not significantly affect bacterial diversity or relative abundances of bacterial classes; however, seasonal environmental changes did. Repeated rhizosphere-targeted applications of B. subtilis QST713 appear to have established the bacterium into the rhizosphere, as populations increased between samples, even after applications stopped. These findings suggest that QST713 may reduce pathogen pressure when repeatedly applied and can reduce fungicide usage during periods of low PRR pressure.

Bacteria in biofloc technology aquaculture systems: roles and mediating factors

AbstractThe abundance of nitrogen compounds, phosphorous compounds and organic matter in biofloc technology (BFT) aquaculture systems creates an ideal medium for increasing microbial communities and load. The abundance of microbial DNA found in BFT aquaculture systems is hypothesised to be among the greatest in current aquaculture systems. Several factors mediate the bacterial diversity, relative abundance and dynamics in BFT systems. This review focusses on the bacteria in BFT aquaculture systems, their role as food for animals present in the culture and their various relationships with major nutrients. The analytical techniques available for determining bacterial integrity and function are reviewed along with the factors that affect microbial community structure, water quality and production performance. Future investigations to characterise bacteria in BFT aquaculture systems and their roles and mediating factors are suggested.

Haemophilus pittmaniae and Leptotrichia spp. Constitute a Multi-Marker Signature in a Cohort of Human Papillomavirus-Positive Head and Neck Cancer Patients.

ObjectivesHuman papillomavirus (HPV) is a known etiological factor of oropharyngeal head and neck cancer (HNC). HPV positivity and periodontal disease have been associated with higher HNC risk, suggesting a role for oral bacterial species. Our objective was to determine oral microbiome profiles in HNC patients (HPV-positive and HPV-negative) and in healthy controls (HC).MethodsSaliva samples and swabs of buccal mucosa, supragingival plaque, and tongue were collected from HNC patients (N = 23 patients, n = 92 samples) before cancer therapy. Next-generation sequencing (16S-rRNA gene V3–V4 region) was used to determine bacterial taxa relative abundance (RA). β-Diversities of HNC HPV+ (N = 16 patients, n = 64 samples) and HNC HPV– (N = 7 patients, n = 28 samples) groups were compared using PERMANOVA (pMonte Carlo < 0.05). LEfSe discriminant analysis was performed to identify differentiating taxa (Log LDA > 2.0). RA differences were analyzed by Mann–Whitney U-test (α = 0.05). CombiROC program was used to determine multi-marker bacterial signatures. The Microbial Interaction Network Database (MIND) and LitSuggest online tools were used for complementary analyses.ResultsHNC vs. HC and HNC HPV+ vs. HNC HPV– β-diversities differed significantly (pMonte Carlo < 0.05). Streptococcus was the most abundant genus for HNC and HC groups, while Rothia mucilaginosa and Haemophilus parainfluenzae were the most abundant species in HNC and HC patients, respectively, regardless of antibiotics treatment. LEfSe analysis identified 43 and 44 distinctive species for HNC HPV+ and HNC HPV– groups, respectively. In HNC HPV+ group, 26 periodontal disease-associated species identified by LefSe had a higher average RA compared to HNC HPV– group. The significant species included Alloprevotella tannerae, Fusobacterium periodonticum, Haemophilus pittmaniae, Lachnoanaerobaulum orale, and Leptotrichia spp. (Mann–Whitney U-test, p < 0.05). Of 43 LEfSe-identified species in HPV+ group, 31 had a higher RA compared to HPV– group (Mann–Whitney U-test, p < 0.05). MIND analysis confirmed interactions between Haemophilus and Leptotrichia spp., representing a multi-marker signature per CombiROC analysis [area under the curve (AUC) > 0.9]. LitSuggest correctly classified 15 articles relevant to oral microbiome and HPV status.ConclusionOral microbiome profiles of HNC HPV+ and HNC HPV– patients differed significantly regarding periodontal-associated species. Our results suggest that oral bacterial species (e.g., Leptotrichia spp.), possessing unique niches and invasive properties, coexist with HPV within HPV-induced oral lesions in HNC patients. Further investigation into host–microbe interactions in HPV-positive HNC patients may shed light into cancer development.

Addition of Lactic Acid Bacteria Can Promote the Quality and Feeding Value of Broussonetia papyrifera (Paper Mulberry) Silage

In this study, the influence of two lactic acid bacteria (LAB) strains [Lactobacillus rhamnosus BDy (LR-BDy) and Lactobacillus buchneri TSy (LB-TSy)] selected from Southwest China on the fermentation characteristics and in vitro gas production of Broussonetia papyrifera (paper mulberry) silage were experimentally explored. The experimental groups were a control group (C), an LB-TSy treatment (LB), an LR-BDy treatment (LR), and an LR-BDy + LB-TSy hybrid group (LR × LB). After the LAB were added, the pH value of paper mulberry silage significantly declined (p &lt; 0.05), and the crude protein content was effectively preserved (p &lt; 0.05). However, no significant changes were found in the levels of neutral detergent fiber, acid detergent fiber, and crude ash (p &gt; 0.05). The lactic acid content in paper mulberry silage was evidently increased (p &lt; 0.05). The in vitro gas production in the LR at 36, 48, and 72 h were markedly higher than that in the other treatments (p &lt; 0.05). Owing to the addition of LAB, the microbial diversity in paper mulberry silage was reduced, while the relative bacterial abundance of Lactobacillus was enhanced. Hence, the addition of LAB selected from the warm and humid region in Southwest China can improve the quality of paper mulberry silage and elevate its feeding value in this region.

Evaluation of the Gastric Microbiome in Patients with Chronic Superficial Gastritis and Intestinal Metaplasia

ObjectiveTo evaluate the gastric microbiome in patients with chronic superficial gastritis (CSG) and intestinal metaplasia (IM) and investigate the influence of Helicobacter pylori (H. pylori) on the gastric microbiome. MethodsGastric mucosa tissue samples were collected from 54 patients with CSG and IM, and the patients were classified into the following four groups based on the state of H. pylori infection and histology: H. pylori-negative CSG (n=24), H. pylori-positive CSG (n=14), H. pylori-negative IM (n=11), and H. pylori-positive IM (n=5). The gastric microbiome was analyzed by 16S rRNA gene sequencing. ResultsH. pylori strongly influenced the bacterial abundance and diversity regardless of CSG and IM. In H. pylori-positive subjects, the bacterial abundance and diversity were significantly lower than in H. pylori-negative subjects. The H. pylori-negative groups had similar bacterial composition and bacterial abundance. The H. pylori-positive groups also had similar bacterial composition but different bacterial relative abundance. The relative abundance of Neisseria, Streptococcus, Rothia, and Veillonella were richer in the I-HP group than in G-HP group, especially Neisseria (t=175.1, P<0.001). ConclusionsThe gastric microbial abundance and diversity are lower in H. pylori- infected patients regardless of CSG and IM. Compared to H. pylori-positive CSG group and H. pylori-positive IM, the relative abundance of Neisseria, Streptococcus, Rothia, and Veillonella is higher in H. pylori-positive patients with IM than in H. pylori-positive patients with CSG, especially Neisseria.

Comparison of the oral microbial composition between healthy individuals and periodontitis patients in different oral sampling sites using 16S metagenome profiling.

The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples. In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis. When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples. In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants

BackgroundThe gut microbiome is important to immune health, metabolism, and hormone regulation. Understanding host–microbiome relationships in captive animals may lead to mediating long term health issues common in captive animals. For instance, zoo managed African elephants (Loxodonta africana) and Asian elephants (Elephas maximus) experience low reproductive rates, high body condition, and gastrointestinal (GI) issues. We leveraged an extensive collection of fecal samples and health records from the Elephant Welfare Study conducted across North American zoos in 2012 to examine the link between gut microbiota and clinical health issues, reproductive hormones, and metabolic hormones in captive elephants. We quantified gut microbiomes of 69 African and 48 Asian elephants from across 50 zoos using Illumina sequencing of the 16S rRNA bacterial gene.ResultsElephant species differed in microbiome structure, with African elephants having lower bacterial richness and dissimilar bacterial composition from Asian elephants. In both species, bacterial composition was strongly influenced by zoo facility. Bacterial richness was lower in African elephants with recent GI issues, and richness was positively correlated with metabolic hormone total triiodothyronine (total T3) in Asian elephants. We found species-specific associations between gut microbiome composition and hormones: Asian elephant gut microbiome composition was linked to total T3 and free thyroxine (free T4), while fecal glucocorticoid metabolites (FGM) were linked to African elephant gut microbiome composition. We identified many relationships between bacterial relative abundances and hormone concentrations, including Prevotella spp., Treponema spp., and Akkermansia spp.ConclusionsWe present a comprehensive assessment of relationships between the gut microbiome, host species, environment, clinical health issues, and the endocrine system in captive elephants. Our results highlight the combined significance of host species-specific regulation and environmental effects on the gut microbiome between two elephant species and across 50 zoo facilities. We provide evidence of clinical health issues, reproductive hormones, and metabolic hormones associated with the gut microbiome structure of captive elephants. Our findings establish the groundwork for future studies to investigate bacterial function or develop tools (e.g., prebiotics, probiotics, dietary manipulations) suitable for conservation and zoo management.