Relative Abundance Of Bacterial Taxa Research Articles

Optimization of the anaerobic digestion process and the metabolic pathway of methanogenesis of Jerusalem artichoke straw with the mixed addition of iron filings and biochar

This study explored the feasibility of the mixed addition of iron filings and biochar in the anaerobic digestion of Jerusalem artichoke straw (JAS), using iron filings and biochar as mixed additives for mid-temperature batch anaerobic digestion experiments, and applied response surface methodology to investigate the interactive effects of different ratios of iron filings and biochar (FE/BC), solid content, and initial pH on the cumulative methane production from JAS. The results showed that the optimal conditions for methane production were an FE/BC of 2.45:7.55, an initial pH of 7.59, and a solid content of 8.80 %. Under these conditions, the cumulative methane production was 278.11 mL g−1 volatile solid (VS) contents, which was very close to the predicted value (286.42 mL g−1 VS), with a relative error of less than 5 %, indicating the effectiveness of the model. The optimized conditions with mixed addition (HB) exhibited good synergistic promotion, increasing cumulative methane production by 48.69 % compared to the control without additives and by 22.29 % and 29.57 % compared to the single addition of iron filings and biochar, respectively. Moreover, the HB treatment under optimized conditions achieved good economic benefits. Metagenomic analysis showed that the relative abundances of bacterial taxa including Fermentimonas, DMER64, Bacteroidetes_VadinHA17, unclassified Synergistaceae, Clostridium, Ruminiclostridium, and unclassified Anaerolineaceae were higher in HB samples, and Methanothrix was also enriched. Methane metabolism pathway analysis indicated that the anaerobic digestion of JAS with the mixed addition of iron filings and biochar enhanced the acetoclastic methane production pathway, thereby increasing methane production.

The relationship of microbial biodiversity and clinical forms of oral lichen planus: analysis based on 16S rRNA sequencing

BACKGROUND: The composition and changes of microbiota have a significant impact on overall health and the development of various diseases. Of particular relevance is the problem of changes in the oral microbiota in patients with lichen planus of the oral mucosa. Studying the relationship between the composition of the oral microbiota and the pathogenesis of oral lichen planus will improve the understanding of the mechanisms of this disease. Thus, this topic is of considerable interest to a wide range of specialists in the field of medicine and biology. AIM: Detailed analysis of oral cavity microbiota and establishment of potential pathogenetic microbial associations with oral lichen planus. MATERIALS AND METHODS: The study included samples from patients diagnosed with various forms of oral red squamous lichen planus (lichen planus erosive-ulcerative) and a control group. The investigation was based on analyzing microbial diversity metrics (alpha and beta diversity), relative abundance of bacterial taxa, and identification of unique bacterial taxa in the oral red squamous lichen planus patients. This analysis utilized the 16S rRNA sequencing method. RESULTS: The analysis revealed a rich bacterial composition in patients with oral lichen planus, which was significantly different from that in the control group. Differences were also observed between the subgroups, especially between the typical and erosive-ulcerative forms of the disease. Notably, beta diversity did not show significant differences between the groups, indicating a similar overall microbiota composition despite fluctuations in the relative abundance of species. Nevertheless, the typical clinical form of the disease demonstrated more significant differences in the microbiota structure compared to the hyperkeratotic and erosive-ulcerative forms. Furthermore, analysis of the study groups revealed the presence of 50% shared microbial species, while the other half was represented by unique species associated with oral lichen planus. Regarding the subgroups, it was found that unique microorganisms correlated with the typical and erosive-ulcerative forms, respectively, providing a deeper understanding of the specific microbiological profile in the context of this disease. CONCLUSION: The study confirmed the hypothesis of an association between the microbiota composition and oral lichen planus, which may be of importance for the development of novel therapeutic approaches.

Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum and ileum in broiler chickens

Coccidiosis, an intestinal disease caused by Eimeria parasites, is responsible for major losses in the poultry industry by impacting chicken health. The gut microbiota is associated with health factors, such as nutrient exchange and immune system modulation, requiring understanding on the effects of Eimeria infection on the gut microbiota. This study aimed to determine the effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum (CeL and CeM) and ileum (IlL and IlM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. E. acervulina infection decreased evenness in CeL microbiota at day 10, increased richness in CeM microbiota at day 3 before decreasing richness at day 14, and decreased richness in IlL microbiota from day 3 to 10. CeL, CeM, and IlL microbiota differed between infected and control birds based on beta diversity at varying time points. Infection reduced relative abundance of bacterial taxa and some predicted metabolic pathways known for short-chain fatty acid production in CeL, CeM, and IlL microbiota, but further understanding of metabolic function is required. Despite E. acervulina primarily targeting the duodenum, our findings demonstrate the infection can impact bacterial diversity and abundance in the cecal and ileal microbiota.

Spatiotemporal variation in the gut microbiomes of co‐occurring wild rodent species

AbstractMammalian gut microbiomes differ within and among hosts. Hosts that occupy a broad range of environments may exhibit greater spatiotemporal variation in their microbiome than those constrained as specialists to narrower subsets of resources or habitats. This can occur if widespread host encounter a variety of ecological conditions that act to diversify their gut microbiomes and/or if generalized host species tend to form large populations that promote sharing and maintenance of diverse microbes. We studied spatiotemporal variation in the gut microbiomes of three co‐occurring rodent species across an environmental gradient in a Kenyan savanna. We hypothesized: (1) the taxonomic, phylogenetic, and functional compositions of gut microbiomes as predicted using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) differ significantly among host species; (2) microbiome richness increases with population size for all host species; and (3) host species exhibit different levels of seasonal change in their gut microbiomes, reflecting different sensitivities to the environment. We evaluated changes in gut microbiome composition according to host species identity, site, and host population size using three years of capture–mark–recapture data and 351 microbiome samples. Host species differed significantly in microbiome composition, though the two species with more specialized diets and higher demographic sensitivities showed only slightly greater microbiome variability than those of a widespread dietary generalist. Total microbiome richness increased significantly with host population size for all species, but only one of the more specialized species also exhibited greater individual‐level microbiome richness in large populations. Across co‐occurring rodent species with diverse diets and life histories, large host population sizes were associated both with greater population‐level microbiome richness (sampling effects) and turnover in the relative abundance of bacterial taxa (environmental effects), but there was no consistent pattern for individual‐level richness (individual specialization). Together, our results show that maintenance of large host populations contributes to the maintenance of gut microbiome diversity in wild mammals.

The Effect of Iron Supplements on the Gut Microbiome of Females of Reproductive Age: A Randomized Controlled Trial

BackgroundIron deficiency is the most common nutritional deficiency worldwide, particularly for young children and females of reproductive age. Although oral iron supplements are routinely recommended and generally considered safe, iron supplementation has been shown to alter the fecal microbiota in low-income countries. Little is known about the effect of iron supplementation on the fecal microbiota in high-income settings. ObjectivesTo assess the effect of oral iron supplementation compared with placebo on the gut microbiome in nonpregnant females of reproductive age in a high-income country. MethodsA 21-d prospective parallel design double-blind, randomized control trial conducted in South Australia, Australia. Females (18–45 y) were randomly assigned to either iron (65.7 mg ferrous fumarate) or placebo. Fecal samples were collected prior to commencing supplements and after 21 d of supplementation. The primary outcome was microbiota β-diversity (paired-sample weighted unique fraction metric dissimilarity) between treatment and placebo groups after 21 d of supplementation. Exploratory outcomes included changes in the relative abundance of bacterial taxa. ResultsOf 82 females randomly assigned, 80 completed the trial. There was no significant difference between the groups for weighted unique fraction metric dissimilarity (mean difference: 0.003; 95% confidence interval: –0.007, 0.014; P = 0.52) or relative abundance of common bacterial taxa or Escherichia-Shigella (q > 0.05). ConclusionsIron supplementation did not affect the microbiome of nonpregnant females of reproductive age in Australia.This trial was registered at clinicaltrials.gov as NCT05033483.

Type VI secretion system drives bacterial diversity and functions in multispecies biofilms

Type VI secretion system (T6SS) plays an essential role in interspecies interactions and provides an advantage for a strain with T6SS in multispecies biofilms. However, how T6SS drives the bacterial community structure and functions in multispecies biofilms still needs to be determined. Using gene deletion and Illumina sequencing technique, we estimated bacterial community responses in multispecies biofilms to T6SS by introducing T6SS-containing Pseudomonas putida KT2440. Results showed that the niche structure shifts of multispecies biofilms were remarkably higher in the presence of T6SS than in the absence of T6SS. The presence of T6SS significantly drove the variation in microbial composition, reduced the alpha-diversity of bacterial communities in multispecies biofilms, and separately decreased and increased the relative abundance of Proteobacteria and Bacteroidota. Co-occurrence network analysis with inferred putative bacterial interactions indicated that P. putida KT2440 mainly displayed strong negative associations with the genera of Psychrobacter, Cellvibrio, Stenotrophomonas, and Brevundimonas. Moreover, the function redundancy index of the bacterial community was strikingly higher in the presence of T6SS than in the absence of T6SS, regardless of whether relative abundances of bacterial taxa were inhibited or promoted. Remarkably, the increased metabolic network similarity with T6SS-containing P. putida KT2440 could enhance the antibacterial activity of P. putida KT2440 on other bacterial taxa. Our findings extend knowledge of microbial adaptation strategies to potential bacterial weapons and could contribute to predicting biodiversity loss and change in ecological functions caused by T6SS.

Characterizing living ocular bacterial communities and the effects of antibiotic perturbation in house finches

AbstractDNA‐based methods to measure the abundance and relative abundance of bacterial taxa can be skewed by the presence of dead or transient bacteria. Consequently, the active, functional members of the community may be a small subset of the detected bacterial community. This mismatch can make inferences about the roles of communities in host health difficult and can be particularly problematic for low‐abundance microbiomes, such as those on conjunctival surfaces. In this study, we manipulated bacterial communities on bird conjunctiva with a bacteriostatic antibiotic, reducing bacterial activity while preserving viability, to identify the living and active conjunctival communities using comparisons of 16S ribosomal DNA and RNA in paired samples. DNA amplicons included many more sequence variants than RNA amplicons from the same communities, with consequent differences in diversity. While we found that changes in communities in DNA samples broadly represent shifts in the living (RNA‐amplicon) communities, assessments of community function may be better described by RNA samples, reducing background noise from dead cells. We further used these data to test RNA:DNA ratios, used in other microbiological contexts, to detect shifts in bacterial activity after antibiotic disruption but were unable to detect changes in bacterial activity with this method.

P1041 Coconut water modulates dietary potassium and gut microbiome to induce remission in ulcerative colitis: randomized controlled trial

Abstract Background High potassium intake is associated with decreased risk of inflammatory bowel disease(IBD), urinary potassium has been correlated with disease activity in ulcerative colitis(UC), and gut microbiome modulation improves outcomes in UC. We evaluated coconut water as potassium rich diet and gut microbiome modulator in patients with mild-moderate UC. Methods This single-center double-blind placebo-controlled trial randomized patients with mild-moderate (simple clinical colitis activity index-SCCAI:3–9) endoscopically active UC (ulcerative colitis endoscopic index of severity-UCEIS>1) in 1:1 ratio to coconut water + standard medical therapy-SMT(CW) vs placebo + SMT. 400ml of coconut water (200-250mg potassium/100ml) was administered for 8 weeks. Primary outcome measure was clinical remission (SCCAI ≤ 2) and secondary outcome measures were clinical response (SCCAI decline ≥ 3) and adverse events at 8 weeks. Microbiome was analyzed at baseline and 8 weeks. Results Of 121 patients screened, 95 were included for modified intention to treat analysis(49-CW, 46-placebo)[mean age-37.2 ± 11.2years; males-54.1%; disease duration-48 (IQR:24–90) months; pancolitis - 26.1%; SCCAI-5 (IQR:4 – 6); UCEIS-4 (IQR:3 – 5)]. There was significant increase in dietary potassium and decline in sodium/potassium ratio at 8 weeks in CW. Clinical response [57.1% vs 28.3%, p=0.01, OR-3.4 (95%CI:1.4 – 7.9)], remission [53.1% vs 28.3%, p=0.02, OR-2.9(95%CI:1.2 – 6.7)] and proportion of patients with fecal calprotectin (FCP)<150μg/g [53.6% vs 14.3%, p=0.01, OR-6.9(95%CI:1.6 – 28.9)] were significantly higher in CW. The relative abundance of bacterial taxa which had a significant or trend towards negative correlation with SCCAI, UCEIS, or FCP, increased at 8 weeks in CW. Adverse events were comparable and no patient developed hyperkalemia. Conclusion Coconut water increased dietary potassium, modulated the gut microbiome and was more effective than placebo for induction of remission in mild-moderate UC.

Coconut Water Induces Clinical Remission in Mild to Moderate Ulcerative Colitis: Double-blind Placebo-controlled Trial

Background and AimsCoconut water is anti-inflammatory, can manipulate the gut microbiome and is a rich source of potassium. Gut microbiome modulation improves outcomes in UC, and potassium possesses in vitro anti-inflammatory property. We evaluated the effect of coconut water as an adjunct therapy for patients with mild-moderate UC. MethodsThis single-center double-blind placebo-controlled trial randomized patients with mild-moderate(simple clinical colitis activity index-SCCAI:3–9) endoscopically active UC(ulcerative colitis endoscopic index of severity-UCEIS>1) in 1:1 ratio to coconut water + standard medical therapy-SMT(CW) vs placebo + SMT. 400ml of coconut water was administered for 8weeks. Primary outcome measure was clinical remission(SCCAI ≤2) and secondary outcome measures were clinical response(SCCAI decline ≥3) and adverse events at 8weeks. Microbiome was analyzed at baseline and 8weeks. ResultsOf 121 patients screened, 95 were included for modified intention to treat analysis(49-CW, 46-placebo)[mean age-37.2±11.2years; males-54.1%; disease duration-48(IQR:24–90)months; pancolitis-26.1%; SCCAI-5(IQR:4 – 6); UCEIS-4(IQR:3 – 5)]. Clinical response[57.1% vs 28.3%, p=0.01, OR-3.4(95%CI:1.4 – 7.9)], remission[53.1% vs 28.3%, p=0.02, OR-2.9(95%CI:1.2 – 6.7)] and proportion of patients with fecal calprotectin(FCP)<150μg/g[30.6% vs 6.5%, p=0.003, OR-6.3(95%CI:1.7 – 23.6)] were significantly higher in CW. The relative abundance of bacterial taxa which had a significant or trend towards negative correlation with SCCAI, UCEIS, or FCP, increased at 8weeks in CW, and this effect was independent of disease activity and dietary fiber. Adverse events were comparable and no patient developed hyperkalemia. ConclusionCoconut water was more effective than placebo for induction of clinical remission in patients with mild to moderate UC.The trial was prospectively registered on clinical trials registry India (No: CTRI/2019/03/01827)

Comparative analysis of the effect of fermented derivatives from Bactrian milk on the gut microbiome

Background:The gut microbiome plays a vital role in maintaining intestinal homeostasis, and its modulation through dietary interventions has garnered considerable interest in improving human health. In this study, we investigated the effect of traditional Kazakh fermented milk products derived from camel milk on the gut microbiome of rats. Objective:The animals were divided into three groups: the Bactrian milk group (BCM), the camel yogurt group (CMY), and the camel cheese group (CMC). Results:After 4 weeks of intervention, the relative abundance of bacterial taxa varied significantly in the BCM and Bactrian milk derivative groups. The CMY group demonstrated a 2-fold increase in the relative abundance of the genus Ligilactobacillus (p=0.032), whereas the CMC group showed a 3-fold decrease (p=0.009). Prevotella_9 exhibited an inverse abundance vector in the CMY (p=0.0005) and CMC (p=0.0001) groups compared to the BCM group. Additionally, 53 metabolic pathways were predicted, each showing varying relative abundances in response to dietary interventions. Notably, the metabolic pathways associated with amines, polyamines, cell structure, fatty acids, and nucleoside and nucleotide biosynthesis underwent the greatest changes. Conclusion:Consumption of camel milk yogurt led to an increase in biodiversity and abundance in the gut microbiota (p&lt;0.01), as evidenced by Shannon and Simpson's indices. In summary, our study demonstrates that fermented camel milk products significantly influence the gut microbiome and metabolic pathways.Keywords: Bactrian camel milk, gut microbiota, rats, yogurt, soft cheese

Chitooligosaccharide enhanced the efficacy of Bacillus amyloliquefaciens CAS02 for the control of tobacco black shank

IntroductionTobacco black shank is a devastating soil-borne disease caused by the oomycete Phytophthora nicotianae, severely hamper tobacco production worldwide. However, the synergistic effect of biocontrol bacteria and marine polysaccharides/oligosaccharides on tobacco black shank control was few documented.MethodsIn this study, Bacillus amyloliquefaciens CAS02 (CAS02) and chitooligosaccharide (COS) were screened firstly, and their synergistic antagonistic effect against P. nicotianae and the underlying mechanism were investigated in vitro and in vivo.ResultsIn vitro experiments showed that, compared with the application of CAS02 or COS alone, co-application of CAS02 and COS significantly increased the inhibition rate against P. nicotianae by 11.67% and 63.31%, respectively. Furthermore, co-application of CAS02 and COS disrupted the structure of mycelia to a greater extent. The co-application of CAS02 and COS showed synergistic effect, with the relative control effect maintained above 60% during the 60-day pot experiment, significantly higher than that of application CAS02 or COS alone. The combined application of CAS02 and COS reduced the relative abundance of P. nicotianae in the rhizosphere soil and increased the relative abundance of bacterial taxa potentially involved in disease suppression, such as Nocardioides, Devosia and Bradyrhizobium. Meanwhile, CAS02 and COS synergistically activated salicylic acid (SA), ethylene (ET), and hypersensitive response (HR) defense signaling pathways in tobacco plants.DiscussionOur findings demonstrate that co-application of CAS02 and COS remarkably improve the relative control effect against tobacco black shank through multiple pathways and provide a promising strategy for the efficient green control of tobacco black shank.

Characterizing alterations in the gut microbiota following postpartum weight change.

Previous research has reported differences in the gut microbiome associated with varying body compositions. More specifically, within populations of mothers, the focus has been on the impact of gestational weight gain. This is the first study to examine postpartum weight change and its association with changes in the gut microbiome, similarly, it is the first to use a Latina cohort to do so. The results support the idea that weight gain may be an important factor in reducing gut microbiome network connectivity, diversity, and changing abundances of specific microbial taxa, all measures thought to impact host health. These results suggest that weight gain dynamically alters mothers' gut microbial communities in the first 6 months postpartum, with comparatively little change in mothers who lost weight; further research is needed to examine the health consequences of such changes.

Alcohol Consumption and the Diversity of the Oral Microbiome in Postmenopausal Women

BackgroundAlcohol reduces neutrophil function and decreases salivary flow, which could affect the composition of the oral microbiome. ObjectiveWe hypothesized that the α- and β-diversity of the oral microbiome and the relative abundance of bacterial taxa would differ by frequency and type of alcohol consumption. MethodsWe used a food frequency questionnaire to assess the frequency of consumption of beer, wine, and liquor (drinks/week) in a sample of 1179 postmenopausal women in the Osteoporosis and Periodontal Disease Study. Women were categorized as nondrinkers, drinking <1 drink/wk, ≥1 to <7 drinks/wk, or ≥7 drinks/wk for total alcohol consumption and for beer, wine, and liquor consumption. The composition and diversity of the oral microbiome was assessed from subgingival plaque samples using 16S ribosomal RNA amplicon sequencing. Permutational multivariate analysis of variance (PERMANOVA) was used to examine β-diversity (between-sample diversity) in the microbiome between alcohol consumption categories. Analysis of covariance was used to examine the mean α-diversity (within-sample diversity), assessed by the Shannon index (species evenness), Chao1 index (species richness), and observed operational taxonomic unit (OTU) count and the mean relative abundance of 245 bacterial taxa across alcohol consumption categories. ResultsOver half of the participants (67%) consumed alcohol, with 14% reporting ≥1 drink/d. The β-diversity across categories of total alcohol consumption, but not categories of alcohol type, was statistically significantly different (P for PERMANOVA = 0.016). Mean α-diversity measures were statistically significantly higher (P < 0.05) in the highest category of total alcohol and wine consumption compared to nondrinkers; no significant associations were found for beer or liquor consumption. The relative abundance of 1 OTU, Selenomonassp._oral_taxon_133, was significantly lower in the highest level of total alcohol consumption compared to nondrinkers after adjustment for multiple comparisons. ConclusionsAlcohol consumption was associated with the diversity and composition of the subgingival microbiome.

Impact of milk secretor status on the fecal metabolome and microbiota of breastfed infants

ABSTRACT Maternal secretor status has been shown to be associated with the presence of specific fucosylated human milk oligosaccharides (HMOs), and the impact of maternal secretor status on infant gut microbiota measured through 16s sequencing has previously been reported. None of those studies have confirmed exclusive breastfeeding nor investigated the impact of maternal secretor status on gut microbial fermentation products. The present study focused on exclusively breastfed (EBF) Indonesian infants, with exclusive breastfeeding validated through the stable isotope deuterium oxide dose-to-mother (DTM) technique, and the impact of maternal secretor status on the infant fecal microbiome and metabolome. Maternal secretor status did not alter the within-community (alpha) diversity, between-community (beta) diversity, or the relative abundance of bacterial taxa at the genus level. However, infants fed milk from secretor (Se+) mothers exhibited a lower level of fecal succinate, amino acids and their derivatives, and a higher level of 1,2-propanediol when compared to infants fed milk from non-secretor (Se-) mothers. Interestingly, for infants consuming milk from Se+ mothers, there was a correlation between the relative abundance of Bifidobacterium and Streptococcus, and between each of these genera and fecal metabolites that was not observed in infants receiving milk from Se- mothers. Our findings indicate that the secretor status of the mother impacts the gut microbiome of the exclusively breastfed infant.

Linking niche size and phylogenetic signals to predict future soil microbial relative abundances.

Bacteria provide ecosystem services (e.g., biogeochemical cycling) that regulate climate, purify water, and produce food and other commodities, yet their distribution and likely responses to change or intervention are difficult to predict. Using bacterial 16S rRNA gene surveys of 1,381 soil samples from the Biomes of Australian Soil Environment (BASE) dataset, we were able to model relative abundances of soil bacterial taxonomic groups and describe bacterial niche space and optima. Hold out sample validated hypothetical causal networks (structural equation models; SEM) were able to predict the relative abundances of bacterial taxa from environmental data and elucidate soil bacterial niche space. By using explanatory SEM properties as indicators of microbial traits, we successfully predicted soil bacterial response, and in turn potential ecosystem service response, to near-term expected changes in the Australian climate. The methods developed enable prediction of continental-scale changes in bacterial relative abundances, and demonstrate their utility in predicting changes in bacterial function and thereby ecosystem services. These capabilities will be strengthened in the future with growing genome-level data.

Types of fiber and gut microbiota composition and diversity among arab females

ObjectivesDietary fiber is recognizedas an important nutrient for gut health. However, research on the relations of different types of fibers (soluble and insoluble) to the human microbiota health is limited. This study aimed to identify whether higher habitual intake of soluble and/or insoluble fiber have a different influence on the composition, diversity, and abundance of microbiota. MethodsWe examined the fecal microbial composition of 92 healthy females aged 18 and above using the novel shotgun metagenomics sequencing technique. The habitual fiber intake was determined using the Saudi food frequency questionnaire. Pearson’s correlation was used for the correlations between total, soluble, and insoluble fiber and gut microbiota. α- and β-diversities were applied to acquire the distinctions in the relative abundances of bacterial taxa. ResultsOur findings show that higher dietary fiber, particularly insoluble fiber, was significantly correlated with the abundances of Bacteroides_u_s, Bacteroides uniformis, and Lactobacillus acidophilus (r = 0.26, 0.29, 0.26, p-value < 0.05, respectively). Non-significant difference was noted in the microbial α-diversity and β-diversity in low and high soluble/insoluble dietary fiber. ConclusionsCurrent findings suggest that insoluble dietary-fiber intake is favorably correlated with the health of the human gut microbiota. However, further investigations are necessary to identify the effect of types of fiber on the specific species identified in this study.

Alterations in nasal microbiota of patients with amyotrophic lateral sclerosis.

Links between alterations in gut microbiota composition and amyotrophic lateral sclerosis (ALS) have previously been reported. This study aimed to examine the microbiota in the nasal cavity of ALS. Sixty-six ALS patients and 40 healthy caregivers who live in close proximity with patients were enrolled. High throughput metagenomic sequencing of the 16S ribosomal deoxyribonucleic acid (rDNA) gene V3-V4 region of nasal microbiota was used to characterize the alpha and beta diversity and relative abundance of bacterial taxa, predict function, and conduct correlation analysis between specific taxa and clinical features. The nasal microbiome of ALS patients showed lower alpha diversity than that of corresponding healthy family members. Genera Gaiella , Sphingomonas , Polaribacter _1, Lachnospiraceae _NK4A136_group, Klebsiella , and Alistipes were differentially enriched in ALS patients compared to controls. Nasal microbiota composition in ALS patients significantly differed from that in healthy subjects (unweighted UniFrac P = 0.001), while Linear discriminant analysis Effect Size (LEfSe) analysis indicated that Bacteroidetes and Firmicutes dominated healthy nasal communities at the phylum level, whereas Actinobacteria was the predominant phylum and Thermoleophilia was the predominant class in ALS patients. Genus Faecalibacterium and Alistipes were positively correlated with ALS functional rating scale revised (ALSFRS-R; rs = 0.349, P = 0.020 and rs = 0.393, P = 0.008), while Prevotella -9 and Bacteroides operational taxonomic units (OTUs) were positively associated with lung function (FVC) in ALS patients ( rs = 0.304, P = 0.045, and rs = 0.300, P = 0.048, respectively). Prevotella -1 was positively correlated with white blood cell counts (WBC, rs = 0.347, P = 0.021), neutrophil percentage (Neu%, rs = 0.428, P = 0.004), and neutrophil-to-lymphocyte ratio (NLR, rs = 0.411, P = 0.006), but negatively correlated with lymphocyte percentage (Lym%, rs = -0.408, P = 0.006). In contrast, Streptococcus was negatively associated with Neu% ( rs = -0.445, P = 0.003) and NLR ( rs = -0.436, P = 0.003), while positively associated with Lym% ( rs = 0.437, P = 0.003). No significant differences in nasal microbiota richness and evenness were detected among the severe and mild ALS patients. ALS is accompanied by altered nasal microbial community composition and diversity. The findings presented here highlight the need to understand how dysbiosis of nasal microbiota may contribute to the development of ALS.

The Early Life Microbiota Is Not a Major Factor Underlying the Susceptibility to Postweaning Diarrhea in Piglets.

Postweaning diarrhea (PWD) in piglets impair welfare, induce economic losses and lead to overuse of antibiotics. The early life gut microbiota was proposed to contribute to the susceptibility to PWD. The objective of our study was to evaluate in a large cohort of 116 piglets raised in 2 separate farms whether the gut microbiota composition and functions during the suckling period were associated with the later development of PWD. The fecal microbiota and metabolome were analyzed by 16S rRNA gene amplicon sequencing and nuclear magnetic based resonance at postnatal day 13 in male and female piglets. The later development of PWD was recorded for the same animals from weaning (day 21) to day 54. The gut microbiota structure and α-diversity during the suckling period were not associated with the later development of PWD. There was no significant difference in the relative abundances of bacterial taxa in suckling piglets that later developed PWD. The predicted functionality of the gut microbiota and the fecal metabolome signature during the suckling period were not linked to the later development of PWD. Trimethylamine was the bacterial metabolite which fecal concentration during the suckling period was the most strongly associated with the later development of PWD. However, experiments in piglet colon organoids showed that trimethylamine did not disrupt epithelial homeostasis and is thus not likely to predispose to PWD through this mechanism. In conclusion, our data suggest that the early life microbiota is not a major factor underlying the susceptibility to PWD in piglets. IMPORTANCE This study shows that the fecal microbiota composition and metabolic activity are similar in suckling piglets (13 days after birth) that either later develop post-weaning diarrhea (PWD) or not, which is a major threat for animal welfare that also causes important economic losses and antibiotic treatments in pig production. The aim of this work was to study a large cohort of piglets raised in separates environments, which is a major factor influencing the early life microbiota. One of the main findings is that, although the fecal concentration of trimethylamine in suckling piglets was associated with the later development of PWD, this gut microbiota-derived metabolite did not disrupt the epithelial homeostasis in organoids derived from the pig colon. Overall, this study suggests that the gut microbiota during the suckling period is not a major factor underlying the susceptibility of piglets to PWD.

Characterization of the oral microbiota among middle-aged men with and without human papillomavirus infection

ObjectivesTo characterize the oral microbiota among middle-aged men and identify differences between men with a prevalent oral high-risk (oncogenic) HPV infection and those without. Materials and MethodsThis was a case-control study nested within a prospective screening study for HPV-related cancers among middle-aged men. 16S rRNA sequencing was used to characterize the oral microbiota and the cobas HPV Test was used to detect presence of oral high-risk HPV types. We determined the overall composition of the oral microbiota and assessed differences in relative abundance of bacterial taxa as well as alpha and beta diversity among men with a prevalent oral high-risk HPV infection compared to men who were HPV-negative. ResultsAmong 13 high-risk HPV-positive and 30 HPV-negative men, we found significant differences in beta diversity but not alpha diversity. Fretibacterium, F0058, Kingella, Treponema, and Prevotella were more abundant among the high-risk HPV-positive men while Neisseria and Lactobacillus were more abundant among the HPV-negative men. ConclusionThis study adds to the evidence that the oral microbiota varies according to oral HPV infection status and may be associated with the natural history of oral HPV infection.

Profiling the gut microbiome unraveled signature bacterial groups in autoimmune diabetes which remain unperturbed regardless of the ionic strength of drinking water

Abstract Type 1 diabetes is an autoimmune disease that occurs spontaneously in non-obese diabetic mice, and the gut microbiota has been implicated in disease manifestation. The simple dietary variable, acidified drinking water, exaggerated or reduced diabetes incidence in some studies but not in our investigation. To elucidate the underlying basis of these discrepancies, we profiled the gut microbiome of diabetic mice that were transitioned from acid to neutral water. Quantitative polymerase reactions using primers specific for 16S rRNA genes validated the relative abundance of bacterial taxa longitudinally from 6 weeks of age to adults that overtly manifested diabetes. Among the 15 representative bacterial groups examined, only Lactobacillussp. remained low throughout the life of the mouse. The frequencies of the Firmicutes Ruminococcaceaeand the Bactereoidetesphylum members Anaerophagasp. and Paludibactersp. increased during maturation. The level of mucin-degrading Akkermansia muciniphila, implicated in diabetes protection remained low throughout the life of the mouse. The segmented filamentous bacteria could be detected in the gut of young mice and remained abundant in adult mice that developed full blown diabetes. The drinking water’s pH neither impacted the relative abundance of these bacterial taxa investigated herein nor diabetes incidence. Thus, the combination of microbiome profiling and quantitative real-time polymerase chain reactions facilitated validation of the signature gut bacterial taxa in autoimmune diabetes, which remain unperturbed by the pH of the drinking water. Supported by the University of Illinois at Chicago, Chicago.