Differences In Beta Diversity Research Articles

Microbiome and Volatile Metabolic Profile of Acetic Acid Fermentation Using Multiple Starters for Traditional Grain Vinegar

Traditional grain vinegar is fermented using multiple acetic acid bacteria (AAB) at various temperatures. A single AAB showed high acid-producing ability at 30 °C with a 5% alcohol concentration and an initial pH adjusted to 4.0. Multiple AAB were similar to a single AAB; however, the optimal initial pH was 3.0. Acid production ability according to the type of AAB was higher in multiple AAB than in single AAB. That is, using multiple AAB helped increase the titratable acidity of traditional grain vinegar. In addition, increasing the titratable acidity and content of volatile flavor compounds was advantageous when two, rather than four, AAB types were mixed and used. The titratable acidity was high at medium temperatures (30 °C); however, volatile flavor compounds increased at low temperatures (20 °C) under multiple AAB. A 16S rDNA-based microbiome taxonomic profiling analysis identified differences in beta diversity due to multiple AAB and fermentation temperatures. In particular, beta diversity analysis revealed a specific pattern when a mixture of Acetobacter ascedens GV–8 and Acetobacter pasteurianus GV–22 was fermented at a low temperature (20 °C). Therefore, we propose the application of multiple AAB with acidic and flavor-producing properties in traditional grain vinegar.

Gastric juice microbiota in pediatric chronic gastritis that clinically tested positive and negative for Helicobacter pylori.

Helicobacter pylori (HP) infection is an identified risk factor for pediatric chronic gastritis (PCG), but its impact on gastric juice microbiota (GJM) remains to be further elucidated in PCG. This study aimed to analyze and compare the microbial communities and microbial interactive networks of GJM in PCG that clinically tested positive and negative for HP (HP+ and HP-, respectively). A total of 45 PCG patients aged from 6 to 16 years were recruited, including 20 HP+ and 25 HP- patients tested by culture and rapid urease test. Gastric juice samples were collected from these PCG patients and subjected to high-throughput amplicon sequencing and subsequent analysis of 16S rRNA genes. While no significant change in alpha diversity, significant differences in beta diversity were observed between HP+ and HP- PCG. At the genus level, Streptococcus, Helicobacter, and Granulicatella were significantly enriched in HP+ PCG, whereas Campylobacter and Absconditabacteriales (SR1) were significantly enriched in HP- PCG. Network analysis showed that Streptococcus was the only genus positively correlated with Helicobacter (r = 0.497) in the GJM network of overall PCG. Moreover, compared to HP- PCG, HP+ PCG showed a reduction in microbial network connectivity in GJM. Netshift analysis identified driver microbes including Streptococcus and other four genera, which substantially contributed to the GJM network transition from HP- PCG to HP+ PCG. Furthermore, Predicted GJM function analysis indicated up-regulated pathways related to the metabolism of nucleotides, carbohydrates, and L-Lysine, the urea cycle, as well as endotoxin peptidoglycan biosynthesis and maturation in HP+ PCG. GJM in HP+ PCG exhibited dramatically altered beta diversity, taxonomic structure, and function, with reduced microbial network connectivity, which could be involved in the disease etiology.

Effects of rare earth as feed additive on production performance, egg quality, serum biochemical parameters, antioxidant capacity, intestinal morphology, and gut microbiota in late-phase laying hens

This study aimed to investigate the effects of dietary rare earth (RE) supplementation on production performance, egg quality, serum biochemical parameters, antioxidant capacity, intestinal morphology, and gut microbiota in late-phase laying hens. A total of 960 Lohmann Pink laying hens (380 d old) were randomly assigned to 1 of 5 dietary treatments in a 21-day feeding trial. There were 6 replicates in each treatment, with 32 hens per replicate. The five experimental diets were supplemented with 0, 150, 300, 450, and 600 g/t RE in the basal diet. Compared with the control group, hens fed the 150 g/t RE diet had a greater average egg weight during the third week of the experimental period (p < 0.05). However, dietary 150, 300, or 600 g/t RE supplementation decreased the eggshell thickness of laying hens compared to that of the control group (p < 0.05). No differences were observed in the serum biochemical parameters of laying hens among treatments except for the HDL-C concentration, which was higher in the 300 or 450 g/t RE-supplemented group than in the control group (p < 0.05). However, GSH-Px activity increased when hens were fed the 600 vs. 0 g/t RE diet (p < 0.05). But dietary supplementation with 600 g/t RE increased the ileum’s crypt depth in laying hens compared to the control group (p < 0.05). There were significant differences in beta diversity of cecum microbiota in laying hens fed a 600 g/t RE diet in place of the other 4 experimental diets (p < 0.05). Compared with the control diet, dietary 600 g/t RE supplementation significantly decreased the relative abundance of Fusobacteriota (phylum) and Fusobacterium (genus) while markedly increasing the relative abundance of Ruminococcus (genus) and Subdoligranulum (genus) (p < 0.05). A high RE dosage negatively affects egg quality and intestinal morphology and alters gut microbiota diversity and composition. In contrast, a moderate RE dosage has beneficial effects on production performance in late-phase laying hens. Further research is warranted regarding eggshell thickness to investigate whether dietary calcium levels must be adjusted when 150 g/t RE is supplemented for late-phase laying hens.

Pruning Wound Protection Products Induce Alterations in the Wood Mycobiome Profile of Grapevines.

Fungal pathogens involved in grapevine trunk diseases (GTDs) may infect grapevines throughout their lifetime, from nursery to vineyard, via open wounds in stems, canes or roots. In vineyards, pruning wound protection products (PWPPs) offer the best means to reduce the chance of infection by GTD fungi. However, PWPPs may affect non-target microorganisms that comprise the natural endophytic mycobiome residing in treated canes, disrupting microbial homeostasis and indirectly influencing grapevine health. Using DNA metabarcoding, we characterized the endophytic mycobiome of one-year-old canes of cultivars Cabernet Sauvignon and Syrah in two vineyards in Portugal and Italy and assessed the impact of established and novel PWPPs on the fungal communities of treated canes. Our results reveal a large fungal diversity (176 taxa), and we report multiple genera never detected before in grapevine wood (e.g., Symmetrospora and Akenomyces). We found differences in mycobiome beta diversity when comparing vineyards (p = 0.01) but not cultivars (p > 0.05). When examining PWPP-treated canes, we detected cultivar- and vineyard-dependent alterations in both alpha and beta diversity. In addition, numerous fungal taxa were over- or under-represented when compared to control canes. Among them, Epicoccum sp., a beneficial genus with biological control potential, was negatively affected by selected PWPPs. This study demonstrates that PWPPs induce alterations in the fungal communities of grapevines, requiring an urgent evaluation of their direct and indirect effects on plants health with consideration of factors such as climatic conditions and yearly variations, in order to better advise viticulturists and policy makers.

Association of the gut microbiome with fecal short-chain fatty acids, lipopolysaccharides, and obesity in young Chinese college students.

Obesity is a growing health problem among young people worldwide and is associated with gut conditions. This study aimed to explore the relationship between obesity, intestinal microbiota, fecal short-chain fatty acids (SCFAs), and lipopolysaccharide (LPS) in young college students. 16S rRNA gene sequences, SCFA and LPS contents, and obesity status were analyzed in 68 young college students (20-25 years old). There were significant differences in intestinal microbial beta diversity among students with different body mass index (BMI). The abundance and proportion of Firmicutes and Bacteroides had no significant correlation with BMI. The contents of butyric acid and valeric acid in the feces of obese students were low, and the content of SCFAs had no significant correlation with BMI and LPS. The content of LPS in the feces of obese people was significantly higher than that in healthy people, and there was a significant positive correlation between LPS content and BMI. In general, there was a correlation between intestinal microbiota, SCFA, LPS, and BMI in young college students. Our results may enrich the understanding of the relationship between intestinal conditions and obesity and contribute to the study of obesity in young college students.

The nasal microbiome in patients suffering from non-steroidal anti-inflammatory drugs-exacerbated respiratory disease in absence of corticosteroids.

Chronic rhinosinusitis (CRS) is a chronic inflammatory disease phenotypically classified by the absence (CRSsNP) or presence of nasal polyps (CRSwNP). The latter may also be associated with asthma and hypersensitivity towards non-steroidal anti-inflammatory drugs (NSAID) as a triad termed NSAID-exacerbated respiratory disease (N-ERD). The role of the microbiome in these different disease entities with regard to the underlying inflammatory process and disease burden is yet not fully understood. To address this question, we measured clinical parameters and collected nasal samples (nasal mucosal fluids, microbiome swabs from middle meatus and anterior naris) of patients suffering from CRSsNP (n=20), CRSwNP (n=20) or N-ERD (n=20) as well as from patients without CRS (=disease controls, n=20). Importantly, all subjects refrained from taking local or systemic corticosteroids or immunosuppressants for at least two weeks prior to sampling. The nasal microbiome was analyzed using 16S rRNA gene amplicon sequencing, and levels of 33 inflammatory cytokines were determined in nasal mucosal fluids using the MSD platform. Patients suffering from N-ERD and CRSwNP showed significantly worse smell perception and significantly higher levels of type 2 associated cytokines IL-5, IL-9, Eotaxin and CCL17. Across all 4 patient groups, Corynebacteria and Staphylococci showed the highest relative abundances. Although no significant difference in alpha and beta diversity was observed between the control and the CRS groups, pairwise testing revealed a higher relative abundance of Staphylococci in the middle meatus in N-ERD patients as compared to CRSwNP (p<0.001), CRSsNP (p<0.01) and disease controls (p<0.05) and of Lawsonella in patients suffering from CRSwNP in middle meatus and anterior naris in comparison to CRSsNP (p<0.0001 for both locations) and disease controls (p<0.01 and p<0.0001). Furthermore, we observed a positive correlation of Staphylococci with IL-5 (Pearson r=0.548) and a negative correlation for Corynebacteria and Eotaxin-3 (r=-0.540). Thus, in patients refraining from oral and nasal corticosteroid therapy for at least two weeks known to alter microbiome composition, we did not observe differences in microbiome alpha or beta diversity between various CRS entities and disease controls. However, our data suggest a close association between increased bacterial colonization with Staphylococci and decreased colonization by Corynebacteria as well as increased type 2 inflammation.

Characterization of rumen microbiome and metabolome from oro-esophageal tubing and rumen cannula in Holstein dairy cows

Less invasive rumen sampling methods, such as oro-esophageal tubing, became widely popular for exploring the rumen microbiome and metabolome. However, it remains unclear if such methods represent well the rumen contents from the rumen cannula technique. Herein, we characterized the microbiome and metabolome in the rumen content collected by an oro-esophageal tube and by rumen cannula in ten multiparous lactating Holstein cows. The 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Untargeted metabolome was characterized using gas chromatography of a time-of-flight mass spectrometer. Bacteroidetes, Firmicutes, and Proteobacteria were the top three most abundant phyla representing ~ 90% of all samples. Although the pH of oro-esophageal samples was greater than rumen cannula, we found no difference in alpha and beta-diversity among their microbiomes. The overall metabolome of oro-esophageal samples was slightly different from rumen cannula samples yet more closely related to the rumen cannula content as a whole, including its fluid and particulate fractions. Enrichment pathway analysis revealed a few differences between sampling methods, such as when evaluating unsaturated fatty acid pathways in the rumen. The results of the current study suggest that oro-esophageal sampling can be a proxy to screen the 16S rRNA rumen microbiome compared to the rumen cannula technique. The variation introduced by the 16S rRNA methodology may be mitigated by oro-esophageal sampling and the possibility of increasing experimental units for a more consistent representation of the overall microbial population. Studies should consider an under or over-representation of metabolites and specific metabolic pathways depending on the sampling method.

Abstract 2883: Gut microbiome dysbiosis promotes immune suppression and lung cancer development

Abstract Mounting evidence supports synergistic roles for the gut microbiome in cancer progression. Yet, the interplay between the gut microbiome and immune responses in cancer is still poorly understood. We recently showed that gut microbiome changes are closely associated with development of Kras-mutant lung adenocarcinoma (KM-LUAD) in a human-relevant, tobacco-associated mouse model (Gprc5a-/-; G). Knockout of the antimicrobial protein Lcn2 in these mice (Gprc5a-/-/Lcn2-/-; GL) further reduced microbial diversity while enhancing inflammation and tumor development. We thus hypothesized that microbial dysbiosis in the gut, such as that incurred by loss of Lcn2, may exacerbate LUAD development. Here, we investigated the effects of gut microbiome modulation on LUAD pathogenesis using fecal microbiota transfer (FMT) in both syngeneic and tobacco carcinogenesis models. Syngeneic G mice (transplant of G LUAD cells) that received FMT from GL donors (G &amp;lt; GL) exhibited significantly increased tumor growth relative to littermates with FMT from G mice (G &amp;lt; G). These effects were recapitulated in an independent syngeneic model (KrasG12D LKR13 cells in wild type mice). Tobacco carcinogen-exposed G &amp;lt; GL mice also exhibited increased lung tumor development compared with similarly exposed G &amp;lt; G littermates. 16S rDNA-Seq analysis of fecal pellets revealed significant differences in gut beta diversity between syngeneic G &amp;lt; G and G &amp;lt; GL mice. G &amp;lt; GL mice additionally displayed elevated relative abundance of tumor-promoting Alistipes, while Ruminoccocus and Akkermansia, taxa associated with favorable response to immunotherapy, were reduced. We next performed single-cell RNA-sequencing to comprehensively probe the tumor immune microenvironment (TIME) and the immune milieu near the gut of tumors and mesenteric lymph nodes (MLNs), respectively. The TIME in G &amp;lt; GL mice displayed an overall enhanced immunosuppressive phenotype evidenced by prominently increased fractions of T regulatory and Cd4+ Izumo1r+ exhausted T cells and, conversely, reduced levels of activated Isg15+ Cd8a+ T cells. MLNs from G &amp;lt; GL mice showed markedly increased fractions of memory B cells expressing the immunosuppressor Bank1 and reduced levels of follicular B cells and Cd8a+ Clec9a+ class 1 dendritic cells (cDC1). Flow cytometry further showed enhanced immunosuppression in G &amp;lt; GL relative to G &amp;lt; G mice, including increased fractions of myeloid-derived suppressor cells in the TIME of the former group. Our findings show that gut microbiome dysbiosis fosters lung cancer development by promoting immunosuppression, perhaps via a local and systemic gut microbiota-immune system crosstalk. Modulating the gut microbiome may be a promising strategy for interception or early treatment of lung cancer. Citation Format: Zahraa Rahal, Fuduan Peng, Yuejiang Liu, Matthew C. Ross, Ansam Sinjab, Ke Liang, Jiping Feng, Chidera O. Chukwuocha, Manvi Sharma, Elizabeth Tang, Camille Abaya, Joseph Petrosino, Junya Fujimoto, Seyed Javad Moghaddam, Linghua Wang, Kristi L. Hoffman, Humam Kadara. Gut microbiome dysbiosis promotes immune suppression and lung cancer development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2883.

Staircase Wetlands for the Treatment of Greywater and the Effect of Greywater on Soil Microbes

Fresh water is an increasingly scarce resource in both urban and rural development. As a response to this challenge, non-potable water reuse is on the rise. This research explored a potential off-grid system for water purification, consisting of a staircase wetland with terracotta pot plants working as a filter for greywater. This study further investigated the physicochemical properties of greywater and the soil before and after wetland purification. The removal of total suspended solids, total coliforms, fecal coliforms, etc., was always between 90 and 99%. Results show that the filtered water satisfied all requirements for water reuse, e.g., a pH of 7–7.5 and a turbidity &lt; 5 NTU. This research then uniquely investigated the effect of greywater on soil microbes and soil biomass using soil DNA extraction and the tea bag index testing method. The filtered greywater absorbed by soil decomposed the soil faster (66% for green tea) and stabilized it better compared to tap-water-absorbed soil or unfiltered greywater. DNA generation sequencing revealed no significant differences in alpha diversity between the control and treatment samples. The beta diversity differences were significant. This nature-based solution can lead to reduced loads on the sewage system, resulting in less wastewater generation.

THE ONSET AND SEVERITY OF ULCERATIVE COLITIS IN IL-10 -/- MICE IS NOT DEPENDENT ON FECAL MICROBIOTA TRANSPLANTATION FROM ULCERATIVE COLITIS PATIENTS

Inflammatory bowel disease (IBD) is a chronic inflammatory condition that affects around 1% of the U.S population. IBD is comprised of Chron’s Disease and Ulcerative Colitis (UC), with UC having a higher incidence rate. IBD is believed to be caused by immune dysfunction and several environmental factors. Specifically in UC, bacterial dysbiosis is positively correlated with colitis severity and incidence. Thus, we propose that genetically susceptible mice colonized with human colitis-associated bacteria will exhibit early onset and increased colitis severity compared to mice colonized with fecal microbiota from healthy individuals. To test this hypothesis, germ-free IL-10-/- mice of an average age of 20 weeks were gavaged orally with fecal samples from healthy individuals and a severe colitis patient with a fecal calprotectin level of 1947 ug/mg. The Disease Activity Index (DAI) was calculated based on occult blood, weight loss, stool consistency, and grimace. DAI was used to assess colitis severity weekly in transplanted mice for eight weeks.16S rRNA sequencing analysis showed a significant difference in alpha (Shannon Index) and beta diversity (unweighted UniFrac) between the colitis patient and healthy donors indicating dysbiosis (p=.0001; p=.001). The colitis donor had a reduction in species richness. Furthermore, recipient mice clustered with the donors in their bacterial composition. Compared to mice with healthy individual-associated bacteria, colitic-associated bacteria did not significantly increase the colitis incidence or severity in IL-10 -/- mice. Furthermore, there were no significant differences in DAI scores, organ weights, and gut permeability between the treatments. Thus, this study demonstrates that bacterial dysbiosis alone is not sufficient to induce colitis in genetically predisposed mice.

Bacterial gut microbiome differences in adults with ADHD and in children with ADHD on psychostimulant medication

Recent evidence suggests that there is a link between neurodevelopmental disorders, such as attention-deficit hyperactivity disorder (ADHD), and the gut microbiome. However, most studies to date have had low sample sizes, have not investigated the impact of psychostimulant medication, and have not adjusted for potential confounders, including body mass index, stool consistency and diet. To this end, we conducted the largest, to our knowledge, fecal shotgun metagenomic sequencing study in ADHD, with 147 well-characterized adult and child patients. For a subset of individuals, plasma levels of inflammatory markers and short-chain fatty acids were also measured. In adult ADHD patients (n = 84), compared to controls (n = 52), we found a significant difference in beta diversity both regarding bacterial strains (taxonomic) and bacterial genes (functional). In children with ADHD (n = 63), we found that those on psychostimulant medication (n = 33 on medication vs. n = 30 not on medication) had (i) significantly different taxonomic beta diversity, (ii) lower functional and taxonomic evenness, (iii) lower abundance of the strain Bacteroides stercoris CL09T03C01 and bacterial genes encoding an enzyme in vitamin B12 synthesis, and (iv) higher plasma levels of vascular inflammatory markers sICAM-1 and sVCAM-1. Our study continues to support a role for the gut microbiome in neurodevelopmental disorders and provides additional insights into the effects of psychostimulant medication. However, additional studies are needed to replicate these findings and examine causal relationships with the disorder.

Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens.

The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.

Changes of gut microbiota and tricarboxylic acid metabolites may be helpful in early diagnosis of necrotizing enterocolitis: A pilot study.

We aimed to explore the value of gut microbiota and tricarboxylic acid (TCA) metabolites in early diagnosis of necrotizing enterocolitis (NEC) among infants with abdominal manifestations. Thirty-two preterm infants with abdominal manifestations at gestational age ≤ 34 weeks were included in the study and were divided into non-NEC (n = 16) and NEC (n = 16) groups. Faecal samples were collected when the infants were enrolled. The gut microbiota was analysed with high-throughput sequencing, and TCA metabolites were measured with multiple reaction monitoring (MRM) targeted metabolomics. Receiver operating characteristic (ROC) curves were generated to explore the predictive value of the obtained data. There was no significant difference in alpha diversity or beta diversity between the two groups (p > 0.05). At the phylum level, Proteobacteria increased, and Actinomycetota decreased in the NEC group (p < 0.05). At the genus level, Bifidobacterium and Lactobacillaceae decreased significantly, and at the species level, unclassified Staphylococcus, Lactobacillaceae and Bifidobacterium animalis subsp. lactis decreased in the NEC group (p < 0.05). Further Linear discriminant analysis effect sizes (LEfSe) analysis showed that the change in Proteobacteria at the phylum level and Lactobacillaceae and Bifidobacterium at the genus level scored higher than 4. The concentrations of succinate, L-malic acid and oxaloacetate in the NEC group significantly increased (p < 0.05), and the areas under the ROC curve for these metabolites were 0.6641, 0.7617, and 0.7344, respectively. Decreased unclassified Staphylococcus, Lactobacillaceae and Bifidobacterium animalis subsp. lactis at the species level as well as the increase in the contents of some TCA metabolites, including succinate, L-malic acid and oxaloacetate, have potential value for the early diagnosis of NEC.

Drivers of Insect Community Change along the Margins of Mountain Streams in Serra da Estrela Natural Park (Portugal).

Mountain ecosystems are important biodiversity hotspots and valuable natural laboratories to study community assembly processes. Here, we analyze the diversity patterns of butterflies and odonates in a mountainous area of high conservation value-Serra da Estrela Natural Park (Portugal)-and we assess the drivers of community change for each of the two insect groups. The butterflies and odonates were sampled along 150 m transects near the margins of three mountain streams, at three elevation levels (500, 1000, and 1500 m). We found no significant differences in odonate species richness between elevations, but marginal differences (p = 0.058) were found for butterflies due to the lower number of species at high altitudes. Both insect groups showed significant differences in beta diversity (βtotal) between elevations, with species richness differences being the most important component for odonates (βrich = 55.2%), while species replacement drove the changes between butterfly assemblages (βrepl = 60.3%). Climatic factors, particularly those depicting harsher conditions of temperature and precipitation, were the best predictors of total beta diversity (βtotal) and its components (βrich, βrepl) for the two study groups. The study of insect biodiversity patterns in mountain ecosystems and of the role played by different predictors contribute to further our understanding on the community assembly processes and may help to better predict environmental change impacts on mountain biodiversity.

Gut Microbiota Composition in the First and Third Trimester of Pregnancy among Malay Women is Associated with Body Mass Index: A Pilot Study.

This study has analysed the pattern of gut microbiota during the first and third trimesters among pregnant Malay women. This was a pilot prospective observational study involving 12 pregnant Malay women without any endocrine disorders and on neither antibiotics nor probiotics. Demographic details and anthropometric measurements were obtained, and the faecal 16S ribosomal ribonucleic acid (rRNA) metagenome microbiota of the first and third trimesters (T1 and T3) were analysed. Univariate and multivariate statistics, partial least squares discriminant analysis (PLSDA) and Kendall rank correlation testing were used to identify key genera and associations with pregnancy trimester and body mass index (BMI). The most abundant phyla were Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria, with significant differences in composition at the genus level demonstrated between T1 and T3. Sequencing showed a statistically significant difference in beta diversity between normal and abnormal BMI at all taxonomic ranks (R 2 = 0.60; Q 2 = 0.23) and genus levels (R 2 = 0.57; Q 2 = 0.37). The relative abundances of Akkermansia (P < 0.05; false discovery rate [FDR] < 0.05), Olsenella (P < 0.05; FDR < 0.05) and Oscillospira (P < 0.05; FDR < 0.05) were found to be significantly higher in normal BMI cases by 2.4, 3.4 and 3.1 times, respectively. Three genera (Akkermansia, Olsenella and Oscillospira) were correlated with normal BMI during pregnancy. All three could be promising biotherapeutic targets in body weight regulation during pregnancy, subsequently reducing complications associated with higher BMI.

Post-weaning diarrhea in pigs from a single Danish production herd was not associated with the pre-weaning fecal microbiota composition and diversity.

The association between the porcine pre-weaning gut microbiota composition and diversity, and subsequent post-weaning diarrhea (PWD) susceptibility is currently being studied. In this longitudinal study, we examined the association between pre-weaning fecal microbiome composition and diversity, and PWD development in a Danish sow herd. Forty-five pigs were followed from birth until 7 days after weaning (post-natal day (PND) 33). At PND 33, the pigs were categorized as PWD cases or healthy controls based on fecal consistency. We compared their fecal microbiomes at PND 8, late lactation (PND 27) and 7 days post weaning (PND 33) using 16S rRNA V3 region high-throughput sequencing. At PND 27 and 33, we also weighed the pigs, assessed fecal shedding of hemolytic Escherichia coli by culture and characterized hemolytic isolates by ETEC virulence factors with PCR and by whole genome sequencing. A total of 25 out of 45 pigs developed PWD and one Enterotoxigenic E. coli strain with F18:LT:EAST1 virotype was isolated from most pigs. At PND 33, we found differences in beta diversity between PWD and healthy pigs (R2 = 0.027, p = 0.009) and that body weight was associated with both alpha and beta diversity. Pre-weaning fecal microbiome diversity did not differ between PWD and healthy pigs and we found no significant, differentially abundant bacteria between them. In the production herd under study, pre-weaning fecal microbiome diversity and composition were not useful indicators of PWD susceptibility.

Estuarine Sediment Microbiomes from a Chronosequence of Restored Urban Salt Marshes.

Salt marshes play an important role in the global nutrient cycle. The sediments in these systems harbor diverse and complex bacterial communities possessing metabolic capacities that provide ecosystem services such as nutrient cycling and removal. On the East Coast of the USA, salt marshes have been experiencing degradation due to anthropogenic stressors. Salt marsh islands within Jamaica Bay, New York City (USA), are surrounded by a large highly urbanized watershed and have declined in area. Restoration efforts have been enacted to reduce further loss, but little is known about how microbial communities develop following restoration activities, or how processes such as nitrogen cycling are impacted. Sediment samples were collected at two sampling depths from five salt marsh islands to characterize the bacterial communities found in marsh sediment including a post-restoration chronosequence of 3-12 years. We used 16s rRNA amplicon sequencing to define alpha and beta diversity, taxonomic composition, and predicted metabolic profile of each sediment sample. We found significant differences in alpha diversity between sampling depths, and significant differences in beta diversity, taxonomic composition, and predicted metabolic capacity among the five sampling locations. The youngest restored site and the degraded natural sampling site exhibited the most distinct communities among the five sites. Our findings suggest that while the salt marsh islands are located in close proximity to each other, they harbor distinct bacterial communities that can be correlated with post-restoration age, marsh health, and other environmental factors such as availability of organic carbon. IMPORTANCE: Salt marshes play a critical role in the global nutrient cycle due to sediment bacteria and their metabolic capacities. Many East Coast salt marshes have experienced significant degradation over recent decades, thought largely to be due to anthropogenic stressors such as nitrogen loading, urban development, and sea-level rise. Salt marsh islands in Jamaica Bay (Queens/Brooklyn NY) are exposed to high water column nitrogen due to wastewater effluent. Several receding marsh islands have been subjected to restoration efforts to mitigate this loss. Little is known about the effect marsh restoration has on bacterial communities, their metabolic capacity, or how they develop post-restoration. Here, we describe the bacterial communities found in marsh islands including a post-restoration chronosequence of 3-12 years and one degraded marsh island that remains unrestored. We found distinct communities at marsh sites, despite their geographic proximity. Differences in diversity and community composition were consistent with changes in organic carbon availability that occur during marsh development, and may result in differences in ecosystem function among sites.

Saccharomyces cerevisiae fermentation product improves robustness of equine gut microbiome upon stress.

Nutritional and environmental stressors can disturb the gut microbiome of horses which may ultimately decrease their health and performance. We hypothesized that supplementation with a yeast-derived postbiotic (Saccharomyces cerevisiae fermentation product-SCFP) would benefit horses undergoing an established model of stress due to prolonged transportation. Quarter horses (n = 20) were blocked based on sex, age (22 ± 3 mo) and body weight (439 ± 3 kg) and randomized to receive either a basal diet of 60% hay and 40% concentrate (CON) or the basal diet supplemented with 21 g/d Diamond V TruEquine C (SCFP; Diamond V, Cedar Rapids, IA) for 60 days. On day 57, horses were tethered with their heads elevated 35cm above wither height for 12 h to induce mild upper respiratory tract inflammation. Fecal samples were collected at days 0, 28, and 56 before induction of stress, and at 0, 12, 24, and 72 h post-stress and subjected to DNA extraction and Nanopore shotgun metagenomics. Within sample (alpha) diversity was evaluated by fitting a linear model and between sample (beta) diversity was tested with permutational ANOVA. The SCFP stabilized alpha diversity across all time points, whereas CON horses had more fluctuation (P < 0.05) at 12, 24, and 72 h post-challenge compared to d 56. A significant difference between CON and SCFP was observed at 0 and 12 h. There was no difference in beta-diversity between SCFP and CON on d 56. Taken together, these observations led us to conclude that treatment with SCFP resulted in more robust and stable microbial profiles in horses after stress challenge.

An Exploratory Case-Control Study on the Associations of Bacterially-Derived Vitamin K Forms with the Intestinal Microbiome and Obesity-Related Osteoarthritis

BackgroundEvidence suggests that natural metabolites produced by intestinal microorganisms may have beneficial or harmful effects on osteoarthritis (OA). This could include menaquinones, which are bacterially-synthesized, biologically-active vitamin K forms abundant in the intestinal microbiome. ObjectivesThe overall goal of this study was to evaluate the association of intestinally-derived menaquinones with obesity-related OA. MethodsThis case-control study used data and biospecimens derived from a subgroup of Johnston County Osteoarthritis Study participants. Fecal menaquinone concentrations and microbial composition were determined in 52 obese participants with hand and knee OA and 42 age- and sex-matched obese participants without OA. The inter-relationships among fecal menaquinones were evaluated using principal component analysis. The differences in alpha and beta diversities and microbial composition across menaquinone clusters were evaluated using ANOVA. ResultsThe samples were clustered into the following 3 groups: cluster 1 characterized by higher fecal menaquinone-9 and -10 concentrations, cluster 2 characterized by lower overall menaquinone concentrations, and cluster 3 characterized by higher menaquinone-12 and -13 concentrations. Overall, fecal menaquinone clusters did not differ between participants with or without OA (P = 0.707). Microbial diversity did not differ across the fecal menaquinone clusters (all F-test P > 0.12). However, the relative abundance of bacterial taxa differed among clusters, with higher abundance of Coprococcus, Prevotella, and Eggerthella in cluster 2 than in cluster 1; higher abundance of Oscillospira, Dorea, Eubacterium, and Bacteroides in cluster 3 than in cluster 1; and higher abundance of Prevotella, Sutterella, and Dorea in cluster 3 than in cluster 2 (all P < 0.001). ConclusionMenaquinones were variable and abundant in the human gut, but the fecal menaquinone clusters did not differ with OA status. Although the relative abundance of specific bacterial taxa differed among fecal menaquinone clusters, the relevance of these differences with respect to vitamin K status and human health is uncertain.

Contribution of preoperative gut microbiota in postoperative neurocognitive dysfunction in elderly patients undergoing orthopedic surgery.

To investigate the role of gut microbiota and metabolites in POCD in elderly orthopedic patients, and screen the preoperative diagnostic indicators of gut microbiota in elderly POCD. 40 elderly patients undergoing orthopedic surgery were enrolled and divided into Control group and POCD group following neuropsychological assessments. Gut microbiota was determined by 16S rRNA MiSeq sequencing, and metabolomics of GC-MS and LC-MS was used to screen the differential metabolites. We then analyzed the pathways enriched by metabolites. There was no difference in alpha or beta diversity between Control group and POCD group. There were significant differences in 39 ASV and 20 genera bacterium in the relative abundance. Significant diagnostic efficiency analyzed by the ROC curves were found in 6 genera bacterium. Differential metabolites in the two groups including acetic acid, arachidic acid, pyrophosphate etc. were screened out and enriched to certain metabolic pathways which impacted the cognition function profoundly. Gut microbiota disorders exist preoperatively in the elderly POCD patients, by which there could be a chance to predict the susceptible population. [http://www.chictr.org.cn/edit.aspx?pid=133843&htm=4], identifier [ChiCTR2100051162].