Abundant Operational Taxonomic Units Research Articles

Dietary Haematococcus pluvialis promotes growth of red swamp crayfish Procambarus clarkii (Girard, 1852) via positive regulation of the gut microbial co-occurrence network

Plant protein served as an alternative protein source to fish meal is widely used in the feed of Procambarus clarkii, but its excessive use has adverse impacts on aquatic animals. Haematococcus pluvialis has great potential for food applications due to its abundant astaxanthin. This experiment investigated the effects of dietary H. pluvialis on growth performance and gut microbiota of P. clarkii. That dietary H. pluvialis significantly increased weight gain rate (WGR), specific growth rate (SGR), and haemolymph immune-related enzyme activities was presented (P < 0.05), accompanied by a decrease in malondialdehyde (MDA) content. Moreover, dietary H. pluvialis reversed microbial dysbiosis and gut immune damage due to the decreased abundance of operational taxonomic unit (OTU) (s__Bacteroidaceae_bacterium_MS4), where interactions within the co-occurrence network restored gut villus development and microbial community stability. Thus, 0.6% H. pluvialis powder was recommended to be included in the feed. It was initially revealed that dietary H. pluvialis helped to stabilize microbial homeostasis, providing a scientific basis for the development of a functional feed.

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin.

Mycoplasma pneumoniae is one of the most important pathogens causing community acquired pneumonia in children, and the pathogenic mechanism of M. pneumoniae infection is complex. Azithromycin is an effective agent for treating the acquired lower respiratory tract infection and urogenital tract infection with slight adverse reactions. This study aimed to compare the intestinal microflora before (PP1) and after azithromycin intervention (PP2) in children with pneumonia caused by M. pneumoniae, combined with body fluid biochemical analysis to determine the intestinal flora affecting the progress of the disease. Fifteen children diagnosed with M. pneumoniae pneumonia were recruited. The fecal samples and clinical biochemical data were collected. 16S rRNA gene amplicon sequencing and bioinformatics analysis were conducted by the Beijing Genomics Institute. The operational taxonomic unit abundance analysis showed significant differences between the two groups. The species richness analysis showed differences in class, family, genus, order, species, and phylum. The abundance of Haemophilus, Pasteurellales, and Pasteurellaceae was found to be significantly higher in the PP1 group. The Pearson correlation analysis showed that the microbes strongly correlated with the clinical features. 16S rRNA gene sequencing data revealed altered composition of gut microbiota in children with M. pneumoniae pneumonia treated with azithromycin. The altered expression of microbes correlated with clinical features, which might help diagnose and treat the disease.

Interaction between bacterial diversity and biogenic amines production in a salted mackerel stored at soft frozen (-7℃-0℃) storage.

The bacterial diversity of salted mackerel “one‐night courtyard” at soft frozen area (−7℃–0℃) storage was studied. The fish samples at 0, 14, 21, 28, and 35 days were analysis for bacterial structure using high‐throughput sequencing technologies (HTS) and biogenic amines using high‐performance liquid chromatography (HPLC). The analysis results of HTS showed that the dominant bacteria species was varied gradually following with storage time. On the 0th, 21st, and 28th days of storage, dominant Vibrionaceae was accounting for 71.70%, 59.16%, and 70.68% of the total sequences analyzed, respectively. On the 14th and 35th days, Shewanellaceae was the dominant bacterial, accounting for 87.53% and 70.95% of the total sequences analyzed, respectively. In addition, 21st and 28th days, an abundance of Operational Taxonomic Units (OTUs) was top. The dominant bacterial of Proteobacteria, Firmicutes, was producer of biogenic amines. Furthermore, the analysis results of HPLC shown the total biogenic amines of maximum amount 363.01 mg/kg in the sample of HY.14 lower than 1000 mg/kg of the FDA regulation. The range ability of cadaverine was obvious following with the storage time. Cadaverine was 87.36 mg/kg on the 0th day, and it was maximum amount of 276.89 mg/kg on the 14th days. Putrescine was 20 mg/kg on the 0th day and maximum amount of 55.04 mg/kg on the 28thdays of storage. The tyramine was smallest amount of production, and the largest amount was 38.99 mg/kg on 28th, and the smallest amount was 11.97 mg/kg on 35th. Nevertheless, the maximum amount of histamine was 55.04 mg/kg on the 0th day and about 23.14 mg/kg of histamine was little change from 14th to 35th days of storage. Dominant bacteria affect the change of biogenic amines. The study can help understand the interaction between microbial flora and biogenic amines in the salted mackerel of one‐night courtyard.

Blood Bacterial DNA Load and Profiling Differ in Colorectal Cancer Patients Compared to Tumor-Free Controls

Simple SummaryIn colorectal cancer patients, epithelial barrier dysfunction can lead to increased intestinal permeability, and gut microbiome was found to vary compared to healthy subjects. We conducted a study to investigate whether bacterial translocation from gastrointestinal tract to bloodstream is associated to intestinal adenoma and/or colorectal cancer. In particular, an epidemiological and metagenomic approach was used to evaluate the relation of the bacterial DNA load and the bacterial taxonomic groups—assessed by 16S rRNA profiling—in blood with the risks of intestinal adenoma and colorectal cancer. These findings can confirm the presence of bacterial DNA in blood in healthy adults and serve as a basis to evaluate new non-invasive techniques for an early CRC diagnosis through the analyses of bacterial DNA circulating in peripheral blood.Inflammation and immunity are linked to intestinal adenoma (IA) and colorectal cancer (CRC) development. The gut microbiota is associated with CRC risk. Epithelial barrier dysfunction can occur, possibly leading to increased intestinal permeability in CRC patients. We conducted a case-control study including 100 incident histologically confirmed CRC cases, and 100 IA and 100 healthy subjects, matched to cases by center, sex and age. We performed 16S rRNA gene analysis of blood and applied conditional logistic regression. Further analyses were based on negative binomial distribution normalization and Random Forest algorithm. We found an overrepresentation of blood 16S rRNA gene copies in colon cancer as compared to tumor-free controls. For high levels of gene copies, community diversity was higher in colon cancer cases than controls. Bacterial taxa and operational taxonomic unit abundances were different between groups and were able to predict CRC with an accuracy of 0.70. Our data support the hypothesis of a higher passage of bacteria from gastrointestinal tract to bloodstream in colon cancer. This result can be applied on non-invasive diagnostic tests for colon cancer control.

Fecal Microbiome and Metabolome Differ in Healthy and Food-Allergic Twins

In this study, the authors characterize fecal microbiomes to identify bacterial taxa and their products that may influence the expression of food allergies in children and adults.Participants included a cohort of 18 twin pairs across a broad age range, 13 of which were discordant twin pairs (one sibling had a food allergy and the other was healthy) and 5 of which were concordant twin pairs (both siblings had a food allergy).First, fecal samples were collected from the twin pairs who lived in the same household, in which they equally avoided the foods to which the affected twin was found to be allergic. 16S ribosomal RNA gene amplicon sequencing was performed on the fecal samples from the 12 discordant twin pairs and 5 concordant twin pairs, and the microbial composition between the twin pairs was compared. For each twin pair, the authors compared the relative abundance of operational taxonomic units (OTUs) and then calculated an OTU correlation score. Next, liquid chromatography-tandem mass spectrometry was used to measure the abundance of metabolic compounds in the same set of fecal samples. Finally, the authors compared the microbial taxa and their metabolites and correlated the data sets to identify any bacterial species or metabolites that may be mechanistically related to health.The healthy and allergic twins exhibited distinct fecal microbial profiles. A bacterial signature of 64 OTUs distinguished healthy from allergic twins; the OTUs enriched in the healthy twins were largely taxa from the Clostridia class. Healthy and allergic twins also exhibit differential enrichment in fecal metabolic pathways, most notably with the enrichment of diacylglycerol in healthy twins. Next, there was a significant association between healthy twins and Phascolarctobacterium faecium and Ruminococcus bromii. These are species from a taxon not previously associated with protection against allergies.Twin pairs exhibited significant differences in their fecal microbiomes and metabolomes through adulthood, suggesting that the gut microbiota may play a protective role in patients with food allergies beyond the infant stage.With this study, the authors are one of the first to offer unique insight into the fecal microbiome and metabolome in allergic and nonallergic patients. By identifying bacterial species and metabolites that may be mechanistically related to health, it may be possible in the future to integrate live microbiome-modulating biotherapies into the treatment of food allergies. Oral immunotherapy, which typically achieves only short-term desensitization and often is accompanied by gastrointestinal symptoms, can potentially be targeted with biotherapeutics to ultimately improve its efficacy and safety. Further investigation is warranted to determine if or how the identified metabolites contribute to protection against allergies.

Investigation of soil nutrients and associated rhizobacterial communities in different sugarcane genotypes in relation to sugar content

BackgroundPlant microbiomes and soil are bridged by rhizobacteria, maintaining and improving plant health and growth in different aspects. This study was conducted in the field station of the Guangxi University, Fusui, China. We investigated soil nutrients, root morphology and rhizosphere bacterial composition, and community structures in 18 sugarcane genotypes concerning sugar content under the same environmental condition.ResultsMost of the rhizosphere microbiomes of these genotypes exhibited similar bacterial compositions. However, the evaluated genotypes harbored a significant effect and difference in the abundance of operational taxonomic units and bacterial composition in the rhizosphere compartments. Alpha diversity analysis on the rhizosphere microbiome showed a significant difference in the bacterial diversity (Shannon index, p < 0.001) and OTU richness (Chao1, p < 0.001). The principal coordinate analysis (PCoA) and hierarchical cluster analysis revealed that the genotype replicated samples grouped, indicating their similarity. Besides, these genotypes also differed significantly in terms of root structure and soil properties. A significant genotypic effect (p < 0.05) was found in the root traits except for rooting depth. The soil chemical properties were significantly different among the evaluated genotypes. Furthermore, sucrose content was strongly correlated with the total root length (TRL) and rooting depth. Genotypes (FN-1702, GUC-3, ZZ-13, ZZ-10, ZZ-6) were the best performing and distinct in bacterial diversity, root structure, soil parameters and sucrose content.ConclusionThe results showed a closely related and highly conserved bacterial community of the rhizosphere microbiome. The rhizosphere microbiome diversity and related bacterial communities were highly associated with the relevant plant taxa, probably at the order level. As a result, it is possible to conclude that the host genotype and the same environmental condition influenced the rhizosphere microbiome via root phenes. Future research regarding plant phenes and microbiome functional groups could be considered an essential factor.Graphic abstract

Effects of influent immigration and environmental factors on bacterial assembly of activated sludge microbial communities

The functional mechanism of microbial assembly of activated sludge (AS) in urban wastewater treatment plants (UWTPs) remains unclear. A comprehensive quantitative evaluation of the contribution of influent immigration and environmental factors to AS community composition requires investigation. In this study, the microbial characteristics of six full-scale UWTPs with different influent compositions and environmental factors (altitude, temperature, dissolved oxygen (DO), pH, chemical oxygen demand (COD), total nitrogen (TN), ammonia nitrogen (NH4+-N), and total phosphorus (TP)) were analyzed to determine the main forces affecting the bacterial assembly of AS microbial communities. Abundant and core taxa were screened out based on the abundance and frequency of operational taxonomic units (OTUs) occurrence in all samples. Abundant OTUs (18.7% occurrence) accounted for 87.7% of the total 16S rRNA sequences, while rare OTUs (71.7% occurrence) accounted for only 7.8% of the total 16S rRNA sequences. A total of 135 OTUs were identified as core taxa, accounting for 14.6–26.2% of the total reads, of which 83 OTUs belonged to abundant taxa. The richness and uniformity of the influent community were significantly lower than those of the AS system. The community composition in influent varied from that in AS. Moreover, about 89.7% (86.5% of 16S rRNA sequences) OTUs in AS samples showed positive growth rates, indicating that immigration of influent communities had a limited effect on the microbial composition of AS. Redundancy analysis (RDA) combined with co-occurrence network showed that the bacterial assembly of microbial communities was significantly correlated with altitude, pH, and TN (P < 0.05), and these three parameters could explain 23.3%, 21.1%, and 17.7% of the bacterial assembly of AS microbial communities in UWTPs, respectively.

Ubiquitous flocculation activity and flocculation production basis of the conglutination mud from Ruditapes philippinarum along the coast of China.

Ruditapes philippinarum conglutination mud (RPM) is a typical waste by-product from manila clam R. philippinarum aquaculture. However, RPM from the clam at an aquaculture farm in Zhoushan, China, has been newly reported as a promising natural bioflocculant resource that contains effective flocculating polysaccharides from the clam associated bacteria. With an intent to figure out whether RPM flocculation activity is ubiquitous to the manila clam across a wide geographical range or only the Zhoushan location, and to explore the flocculation production basis and ultimately widen its exploitation scope, in this study, an extensive survey of RPMs from four representative locations along the coast of China was performed to determine their flocculation activity, polysaccharide constitution and bacterial community composition. Frozen preserved RPM samples from Zhoushan, Dalian, Weihai and Zhanjiang exhibited comparable flocculation activities (FRs) ranging from 61.9±2.4% to 73.2±0.9% at dosage of 8 g·L-1; while fresh RPMs from Zhoushan exhibited a much higher flocculation activity of 91.34±1.18% than its frozen counterpart. Polysaccharide extracts from the four locations showed similar monosaccharide constitutions to some extent. The geographical distribution led to certain variation in bacterial community structures. The similarity clustering of the polysaccharide compositions coincided with that of bacterial community structures from RPMs, suggesting that polysaccharides and respective bacterial communities might be the foundation of the flocculation activity for all RPMs. The overlapping OTUs across all the RPMs accounted for 44.6–62.22% of the overall sequences in each sample and contained the vast majority of the most abundant OTUs (Operational Taxonomic Units), forming a common "core microbiome" that is probably responsible for polysaccharide production and flocculation activity development.

Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods

The diet plays a major role in shaping gut microbiome composition and function in both humans and animals, and dietary intervention trials are often used to investigate and understand these effects. A plethora of statistical methods for analysing the differential abundance of microbial taxa exists, and new methods are constantly being developed, but there is a lack of benchmarking studies and clear consensus on the best multivariate statistical practices. This makes it hard for a biologist to decide which method to use. We compared the outcomes of generic multivariate ANOVA (ASCA and FFMANOVA) against statistical methods commonly used for community analyses (PERMANOVA and SIMPER) and methods designed for analysis of count data from high-throughput sequencing experiments (ALDEx2, ANCOM and DESeq2). The comparison is based on both simulated data and five published dietary intervention trials representing different subjects and study designs. We found that the methods testing differences at the community level were in agreement regarding both effect size and statistical significance. However, the methods that provided ranking and identification of differentially abundant operational taxonomic units (OTUs) gave incongruent results, implying that the choice of method is likely to influence the biological interpretations. The generic multivariate ANOVA tools have the flexibility needed for analysing multifactorial experiments and provide outputs at both the community and OTU levels; good performance in the simulation studies suggests that these statistical tools are also suitable for microbiome data sets.

16S rRNA Gene Sequence Identification of Cultivable-Bacterioplankton Between Ambient Water and Gastrointestinal Tract (GIT) of Resident Teleost.

This study was conducted to evaluate the ambient water bacterial dynamics and its influence on the gut of resident teleosts; Oreochromis niloticus. The bacterial communities in the ambient water and the gastrointestinal tract (GIT) of O. niloticus were profiled using a culture-dependent method and followed by the 16S rRNA gene sequencing. The results indicated bacterial phyla of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes respectively between the two microbial consortia. However, the relative abundance among the bacterial phyla notably differed between the two consortia. The relative abundance of Proteobacteria (≤ 67%) was dominant in both consortia, but contrarily, Actinobacteria and Bacteroidetes were higher in the ambient water relative to the GIT which indicated Proteobacteria and Bacilli as the highest diversity. Nevertheless, the relative abundance of γ-proteobacteria and Bacilli remarkably dominated both consortia at the class level, with Bacillus and Pseudomonas being the most abundant operational taxonomic units (OTUs).

Effects of antibiotics on the development and intestinal bacterial diversity of black soldier fly larvae

The effects of four antibiotics (metronidazole (M) levofloxacin (L), sodium ampicillin (A), and streptomycin sulphate (S)) and their pair-wise combinations at three doses on the development and intestinal bacterial diversity of the black soldier fly (BSF;Hermetia illucens) larvae were studied. At a low dose M and L were able to inhibit larval growth. At a high dose, all antibiotics were shown to inhibit larval growth. However, the pair-wise combinational use of the antibiotics did not effectively enhance the inhibitory effect. The gut bacterial diversity of the normal control (NC) was significantly higher than the antibiotic-treated groups with 737 operational taxonomic units (OTUs) from the larval guts of NC, compared to 305 and 227 from ML and AS. The number of anaerobic bacteria in ML was significantly lower than in NC and AS, with the relative abundance of OTUs from larval guts of ML being only about 0.01, compared to 0.4 for NC and 0.15 for AS. These results indicated that antibiotics at the experimental concentration did not affect the palatability of food for insects, but they would affect the diversity of food and intestinal microorganisms of BSF larvae, and the inhibitory effect of antibiotics on growth and development of BSF larvae displayed in this study was a complex effect.

Distinguishing Features of the Urinary Bacterial Microbiome in Patients with Neurogenic Lower Urinary Tract Dysfunction.

We aimed to characterize the urinary microbiome of catheterizing patients with neurogenic lower urinary tract dysfunction (NLUTD) and to evaluate differences based on type of bladder management or frequency of urinary tract infections. This is a prospective, cross-sectional study of urine samples from asymptomatic, catheterizing patients with neurogenic lower urinary tract dysfunction who used either clean intermittent catheterization or indwelling catheters. Patients without symptoms of urinary tract infection provided a catheterized urine sample for urinalysis, culture and bacterial community microbiome analysis. A total of 95 patients submitted urine for analysis, of whom 69 had sufficient sequence reads (>1,203) for microbiome analysis. Cases with low bacterial signal amplification were associated with use of vaginal estrogen, no intradetrusor botulinum toxin A use and no growth on standard urine culture. The most abundant operational taxonomic units were from the phylum Proteobacteria, classified as Enterobacteriaceae and Escherichia. Alpha diversity varied among those who used indwelling catheters vs clean intermittent catheterization, and those who underwent botulinum toxin A injection vs not. On linear discriminate analysis, the relative abundance of the operational taxonomic units identified as Pseudomonas was higher among patients using indwelling catheters relative to clean intermittent catheterization. The operational taxonomic unit identified as Aerococcus was at a higher relative abundance among males compared to females. Enterobacteriaceae and Escherichia were the most abundant genera in the urinary microbiome of patients with neurogenic lower urinary tract dysfunction. Urinary microbiome diversity varied based on bladder management type. Future clinical correlations between microbiome of neurogenic patients and clinical presentation may help guide treatment strategies.

Characterization of bacterial DNA identified in abscessed and non-abscessed bovine hepatic tissue at the time of harvest.

Bacteriological characterization of bovine liver abscesses has been accomplished by cultural methods but DNA methods are still needed, as many bacteria are not conducive to laboratory culture. In addition to this gap in research, there have been no studies which identify the bacterial presence within healthy, non-abscessed liver tissue. The objective of this study was to compare the bacteriome of both abscessed and non-abscessed bovine livers in an observational case–control study design. Fifty-six livers, obtained from Holstein steers, were scored according to a modified Elanco liver abscess score description where A− was partitioned into active abscesses or scarred where only scars were present. Parenchyma tissue was collected from non-abscessed livers (n = 22) and scarred livers (n = 7), and purulent material was collected from abscessed livers (n = 24), and DNA was extracted for 16s rRNA gene sequence-based bacterial analysis. Across liver samples, 21 total phyla were identified with a mean of 14. Predominant phyla, accounting for >98% of reads, were Fusobacteria (51.7%), Bacteroidetes (26.9%), Proteobacteria (8.03%), Firmicutes (5.39%), Cyanobacteria (3.85%), and Actinobacteria (2.21%). Proteobacteria, Cyanobacteria, and Firmicutes were greater in non-abscessed and scarred livers, whereas Fusobacteria and Bacteroidetes prevailed in abscessed livers. Non-abscessed livers shared 3,059 operational taxonomic units (OTU) with abscessed livers (total OTU of all livers = 4,167), but non-abscessed livers had greater richness and evenness, whereas abscessed livers had greater dominance (P ≤ 0.0014). Liver score affected the relative abundance of OTU (R = 0.463; P = 0.001) but abscessed livers shared ≥ 40% similarity and were not different from each other (P ≥ 0.370). Of the predominant OTU (top 10 as a % of reads), three OTU (Fusobacteria necrophorum, Bacteroides spp., and Trueperella pyogenes) were shared across both abscessed and non-abscessed livers. Fusobacterium necrophorum was the dominant OTU regardless of liver score, and the single most abundant OTU, even among non-abscessed livers. We describe bacterial DNA detected in non-abscessed bovine liver tissue for the first time, which indicates possible presence of viable bacteria with pathogenic potential in apparently healthy liver tissue.

The gastric microbiota in patients with Crohn\u2019s disease; a preliminary study

The gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.

Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.

Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.

Association between the urogenital microbiome and surgical treatment response in women undergoing midurethral sling operation for mixed urinary incontinence

The urogenital microbiome is associated with urgency and mixed urinary incontinence symptoms and differential treatment responses to pharmacotherapy for urgency urinary incontinence. This study aimed to describe whether the preoperative urinary and vaginal microbiomes were associated with surgical treatment responses at 12 months after a midurethral sling operation in women with mixed urinary incontinence. This cohort study compared the preoperative microbiome compositions of urine and vaginal samples from a subset of women undergoing a midurethral sling operation in the Effects of Surgical Treatment Enhanced With Exercise for Mixed Urinary Incontinence trial (NCT01959347) and compared the microbiota in women who were surgical responders vs surgical nonresponders. Twelve-month objective response was defined as a ≥70% reduction from baseline urinary incontinence episodes on a 3-day diary. Subjective response was defined as a change from baseline in the Urogenital Distress Inventory scores. Bacterial abundance and beta diversity were assessed using 16S ribosomal RNA sequencing. The primary differential abundance analysis described predominant bacterial operational taxonomic units associated with responders vs nonresponders using unadjusted and age-adjusted linear models. Objective nonresponders (n=28) compared with responders (n=72) were older (58.5±10.7 vs 51.6±10.2 years) and more likely postmenopausal without hormone use (odds ratio, 6.4; 95% confidence interval, 1.8-22.6). Vaginal and urinary microbiota beta diversities were associated with age (P<.05) for both responders and nonresponders. Overall, predominant operational taxonomic units (genera) were Lactobacillus, Gardnerella, Tepidimonas, Escherichia, Streptococcus, and Prevotella. Operational taxonomic units from baseline urine samples were not significantly associated (P threshold=.05) with surgical treatment responses. A greater abundance of baseline vaginal Lactobacillus was associated with an objective response (P=.04) and Prevotella with an objective nonresponse (P=.01). Adjusting for age, only a greater abundance of baseline vaginal Prevotella was associated with an objective nonresponse (P=.01). Moreover, less abundant vaginal operational taxonomic units were associated with objective and subjective responses and persistent urinary incontinence symptoms (P<.05). Women meeting a 70% reduction of urinary incontinence treatment episodes (objective responders) had greater vaginal Lactobacillus at the time of the surgical procedure; however, controlling for age diminished this association. Women not meeting a 70% reduction of urinary incontinence episodes 1 year after a midurethral sling operation had greater vaginal Prevotella at the time of the midurethral sling operation. Further research is needed to determine whether therapy altering the vaginal microbiome may impact surgical treatment responses in women with mixed urinary incontinence.

Investigating the Effects of a Phytobiotics-Based Product on the Fecal Bacterial Microbiome of Weaned Pigs

Simple SummaryMaintaining gut health during the weaning period remains a major challenge for swine producers. Phytobiotics, which are plant-derived bioactive products for use as supplements in food animals, have shown great promise in helping to stabilize the gut environment of weaned pigs, but their mechanisms of action remain unclear. To determine if the positive impact of phytobiotics on gut health may be by influencing the symbiotic bacteria that inhabit the gut of young pigs, this report describes a comparison between fecal bacterial populations of weaned pigs supplemented with a commercial phytobiotic product for seven days to those of untreated pigs. Together, the results indicate that phytobiotic supplementation may provide a favorable environment for both lactate-producing and lactate-utilizing bacteria.The transition to a solid diet, as well as environmental and social stress, have a direct impact on swine gut physiology during weaning, affecting host gastrointestinal functions, as well as resident symbiotic microbial communities. While plant-derived bioactive products, such as phytobiotics, have shown great potential to mitigate these challenges, providing benefits such as antimicrobial, antioxidant, and anti-inflammatory activities, their mechanisms of action remain largely unexplored. To gain more insight, a 21 day trial is conducted to investigate the effects of LiveXtract, a commercial plant-based product, using fecal samples as a proxy for gut bacteria in weaned pigs. High-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene is used to determine bacterial composition at days 1 (pre-treatment), 4, 10, and 21 postweaning. Our results show that Lactobacillaceae and Peptostreptococcaceae are both higher in the supplemented group at D4 (p < 0.05), while Streptococcaceae are significantly lower in the treated group at D10 and D21. At D10, Erysipelotrichaceae are lower, and Veillonellaceae are higher in the treated samples than the control group (p < 0.05). Of the thirteen abundant Operational Taxonomic Units (OTUs) that have different representation between treated and control pigs (p < 0.05), six are predicted to be lactate producers (affiliation to Lactobacillus or Streptococcus), and one is predicted to be a lactate utilizer, based on its high identity to Megasphaera elsdenii. Together, these data suggest that phytobiotics may provide a favorable metabolic equilibrium between lactate production and utilization. Lactate is considered a critical microbial end product in gut environments, as it can inhibit pathogens or be metabolized to propionate for utilization by host cells.

Diversity and substrate-specificity of green algae and other micro-eukaryotes colonizing amphibian clutches in Germany, revealed by DNA metabarcoding

Amphibian clutches are colonized by diverse but poorly studied communities of micro-organisms. One of the most noted ones is the unicellular green alga, Oophila amblystomatis, but the occurrence and role of other micro-organisms in the capsular chamber surrounding amphibian clutches have remained largely unstudied. Here, we undertook a multi-marker DNA metabarcoding study to characterize the community of algae and other micro-eukaryotes associated with agile frog (Rana dalmatina) clutches. Samplings were performed at three small ponds in Germany, from four substrates: water, sediment, tree leaves from the bottom of the pond, and R. dalmatina clutches. Sampling substrate strongly determined the community compositions of algae and other micro-eukaryotes. Therefore, as expected, the frog clutch-associated communities formed clearly distinct clusters. Clutch-associated communities in our study were structured by a plethora of not only green algae, but also diatoms and other ochrophytes. The most abundant operational taxonomic units (OTUs) in clutch samples were taxa from Chlamydomonas, Oophila, but also from Nitzschia and other ochrophytes. Sequences of Oophila “Clade B” were found exclusively in clutches. Based on additional phylogenetic analyses of 18S rDNA and of a matrix of 18 nuclear genes derived from transcriptomes, we confirmed in our samples the existence of two distinct clades of green algae assigned to Oophila in past studies. We hypothesize that “Clade B” algae correspond to the true Oophila, whereas “Clade A” algae are a series of Chlorococcum species that, along with other green algae, ochrophytes and protists, colonize amphibian clutches opportunistically and are often cultured from clutch samples due to their robust growth performance. The clutch-associated communities were subject to filtering by sampling location, suggesting that the taxa colonizing amphibian clutches can drastically differ depending on environmental conditions.

Typhlitis induced by Histomonas meleagridis affects relative but not the absolute Escherichia coli counts and invasion in the gut in turkeys

Unlike in chickens, dynamics of the gut microbiome in turkeys is limitedly understood and no data were yet published in context of pathological changes following experimental infection. Thus, the impact of Histomonas meleagridis-associated inflammatory changes in the caecal microbiome, especially the Escherichia coli population and their caecal wall invasion in turkeys was investigated. Birds experimentally inoculated with attenuated and/or virulent H. meleagridis and non-inoculated negative controls were divided based on the severity of macroscopic caecal lesions. The high throughput amplicon sequencing of 16SrRNA showed that the species richness and diversity of microbial community significantly decreased in severely affected caeca. The relative abundances of operational taxonomic units belonging to Anaerotignum lactatifermentans, E. coli, and Faecalibacterium prausnitzii were higher and paralleled with a decreased abundances of those belonging to Alistipes putredinis, Streptococcusalactolyticus, Lactobacillus salivarius and Lactobacillus reuteri in birds with the highest lesion scores. Although the relative abundance of E. coli was higher, the absolute count was not affected by the severity of pathological lesions. Immunohistochemistry showed that E. coli was only present in the luminal content of caecum and did not penetrate even severely inflamed and necrotized caecal wall. Overall, it was demonstrated that the fundamental shift in caecal microbiota of turkeys infected with H. meleagridis was attributed to the pathology induced by the parasite, which only led to relative but not absolute changes in E. coli population. Furthermore, E. coli cells did not show tendency to penetrate the caecal tissue even when the intestinal mucosal barriers were severely compromised.

Profiling of Intestinal Microbiota in Patients Infected with Respiratory Influenza A and B Viruses.

Little is known about the association between respiratory viral infections and their impact on intestinal microbiota. Here, we compared the effect of influenza types, A and B, and influenza shedding in patients’ stools on the gut microbiota diversity and composition. Deep sequencing analysis was performed for the V4 region of the 16S rRNA gene. Fecal samples were collected from 38 adults with active respiratory influenza infection and 11 age-matched healthy controls. Influenza infection resulted in variations in intestinal bacterial community composition rather than in overall diversity. Overall, infected patients experienced an increased abundance of Bacteroidetes and a corresponding decrease in Firmicutes. Differential abundance testing illustrated that differences in gut microbiota composition were influenza type-dependent, identifying ten differentially abundant operational taxonomic units (OTUs) between influenza A- and influenza B-infected patients. Notably, virus shedding in fecal samples of some patients had significantly reduced gut bacterial diversity (p = 0.023). Further taxonomic analysis revealed that the abundance of Bacteroides fragilis was significantly higher among shedders compared to non-shedders (p = 0.037). These results provide fundamental evidence of the direct effect of influenza infection on gut microbiota diversity, as reported in patients shedding the virus.