Relative Abundance Of Bacterial Taxa Research Articles

The Association Between Smoking and Gut Microbiome in Bangladesh.

Epidemiological studies that investigate alterations in the gut microbial composition associated with smoking are lacking. This study examined the composition of the gut microbiome in smokers compared with nonsmokers. Stool samples were collected in a cross-sectional study of 249 participants selected from the Health Effects of Arsenic Longitudinal Study in Bangladesh. Microbial DNA was extracted from the fecal samples and sequenced by 16S rRNA gene sequencing. The associations of smoking status and intensity of smoking with the relative abundance or the absence and presence of individual bacterial taxon from phylum to genus levels were examined. The relative abundance of bacterial taxa along the Erysipelotrichi-to-Catenibacterium lineage was significantly higher in current smokers compared to never-smokers. The odds ratio comparing the mean relative abundance in current smokers with that in never-smokers was 1.91 (95% confidence interval = 1.36-2.69) for the genus Catenibacterium and 1.89 (95% confidence interval = 1.39-2.56) for the family Erysipelotrichaceae, the order Erysipelotrichale, and the class Erysipelotrichi (false discovery rate-adjusted p values = .0008-.01). A dose-response association was observed for each of these bacterial taxa. The presence of Alphaproteobacteria was significantly greater comparing current with never-smokers (odds ratio = 4.85, false discovery rate-adjusted p values = .04). Our data in a Bangladeshi population are consistent with evidence of an association between smoking status and dosage with change in the gut bacterial composition. This study for the first time examined the relationship between smoking and the gut microbiome composition. The data suggest that smoking status may play an important role in the composition of the gut microbiome, especially among individuals with higher levels of tobacco exposure.

Valorization of agricultural wastes could improve soil fertility and mitigate soil direct N2O emissions

The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO2 and N2O direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct N2O emissions when treated with agricultural wastes. The highest soil direct N2O emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct N2O emissions. On the contrary, agricultural wastes stimulated CO2 accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil N2O emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with N2O emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced N2O emissions.

Predominance of soil vs root effect in rhizosphere microbiota reassembly.

Rhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants.

Endometrial microbiota in infertile women with and without chronic endometritis as diagnosed using a quantitative and reference range-based method

To systematically compare the endometrial microbiota in infertile women with and without chronic endometritis (CE), as diagnosed by a quantitative and reference range-based method. Case-control observational study. University-affiliated hospital. One hundred and thirty infertile women. Endometrial biopsy and fluid (uterine lavage, UL) collected precisely 7days after LH surge, with plasma cell density (PCD) determined based on Syndecan-1 (CD138)-positive cells in the entire biopsy section and culture-independent massively parallel sequencing of the 16S ribosomal RNA gene performed on both the CE and non-CE endometrial fluid samples. Relative abundance of bacterial taxa. Chronic endometritis was diagnosed if the PCD was above the 95th percentile (>5.15cells per 10mm2) of the reference range in fertile control subjects. With this stringent diagnostic criterion, 12 women (9%) were diagnosed with CE. Sequencing was successfully performed on all endometrial samples obtained by UL) (CE, n = 12; non-CE, n = 118). The median relative abundance of Lactobacillus was 1.89% and 80.7% in the CE and non-CE microbiotas, respectively. Lactobacillus crispatus was less abundant in the CE microbiota (fold-change, range: 2.10-2.30). Eighteen non-Lactobacillus taxa including Dialister, Bifidobacterium, Prevotella, Gardnerella, and Anaerococcus were more abundant in the CE microbiota (fold-change, 2.10-18.9). Of these, Anaerococcus and Gardnerella were negatively correlated in relative abundance with Lactobacillus (SparCC correlation magnitude, range: 0.142-0.177). Chronic endometritis was associated with a statistically significantly higher abundance of 18 bacterial taxa in the endometrial cavity. ChiCTR-IOC-16007882.

Abstract 2830: Breast cancer and the human oral and gut microbiomes

Abstract The human body harbors ten times more bacterial cells than human cells - a stunning figure that suggests a likely dynamic between our bodies and the bacteria we carry, both in health and disease. In this study, we characterized and compared the gut and oral microbiota from women with invasive breast cancer, women with ductal carcinoma in situ (DCIS), and healthy women. Samples were collected prior to any systemic therapy to avoid therapy-associated effects on the microbiomes studied. Kits for collecting oral and stool swab samples were distributed to patients for self-collection. DNA was isolated from these samples and bacterial 16S rRNA was PCR amplified and sequenced. Based on the sequencing results, bacterial taxa present in the samples were enumerated. The gut microbiota of women with breast cancer demonstrated significantly lower alpha-diversity compared to the gut microbiomes of healthy women. In contrast, there was no difference in gut microbiota alpha-diversity of women with DCIS compared to healthy women. There were no differences in alpha-diversity of the oral microbiota between any of the cohorts. Discriminant analysis of principal components (DAPC) at the genus level of both the gut and oral microbiota demonstrated distinct clustering of the DCIS, breast cancer, and healthy cohorts. LEfSe analyses were performed to detect differences in relative abundance of bacterial taxa across the gut and oral samples. The genus Bacteroides was significantly enriched in breast cancer compared to healthy samples, as were the related taxa Bacteroidetes (phylum), Bacteroidia (class), Bacteroidales (order), and Bacteroidaceae (family). The genera Fusicatenibacter and Butyrivibrio, both from the phylum Firmicutes, class Clostridia, order Clostridiales, family Lachnospiraceae, were more abundant in the healthy cohort. Only 2 genera, Fusicatenibacter and Clostridium were differentially abundant between the DCIS and healthy gut samples, both being enriched in the healthy samples. Numerous taxa in the oral microbiota were found to be differentially abundant between cohorts. In particular, 7 genera (Bacteroides, Blautia, Faecalibacterium, Roseburia, Pseudobutyrivibrio, Anaerostipes, and Subdoligranulum) were all significantly enriched in the healthy oral samples compared to the DCIS and breast cancer oral samples. To determine whether the taxonomic differences we observed between the cohorts’ gut and oral microbiota corresponded to functional differences, we performed a predictive functional analysis using Piphillin which identified 35 KEGG pathways differentially present in the gut microbiota and 8 pathways differentially present in the oral samples. Understanding how gut and oral microbiomes relate to breast cancer may open up new opportunities for the development of novel markers for early detection (or markers of susceptibility) as well as new strategies for prevention and/or treatment. Citation Format: Michael J. Campbell, Emma McCune, Breanna Johnson, Tess O'Meara, Diane Heditsian, Susie Brain, Laura Esserman. Breast cancer and the human oral and gut microbiomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2830.

Effects of Lactic Acid Bacteria-Fermented Soymilk on Isoflavone Metabolites and Short-Chain Fatty Acids Excretion and Their Modulating Effects on Gut Microbiota.

Lactobacillus rhamnosus strain ASCC 1520 with high soy isoflavone transformation ability was used to ferment soymilk and added to the diet of mice. The impact of L. rhamnosus fermentation on soy isoflavone metabolites and intestinal bacterial community, in conjunction with fecal enzyme activity and short-chain fatty acids (SCFA) excretion was evaluated. Antibiotics intervention resulted in a decrease in fecal enzyme activities and SCFA. Although long-term intake of soymilk or L. rhamnosus-fermented soymilk did not affect the fecal β-glucuronidase and β-galactosidase activities, it improved the β-glucosidase activity when antibiotics were concomitantly administered. Soymilk or fermented soymilk administration increased the isoflavone metabolites (O-DMA and equol) excreted in urine. Antibiotics decreased the daidzein excretion and its metabolites but showed little effect on glycitein and genistein excretion. Principal coordinates analysis (PCoA) of the 16s rRNA gene sequencing data found a remarkable shift in gut microbiota after soymilk administration and antibiotics treatment. Matastats test of the relative abundance of bacterial taxa revealed Odoribacter (Bacteroidales family), Lactobacillus (Lactobacillales order), and Alistipes (Rikenellaceae family) were enriched in soymilk while bacterial taxa from Bacteroides and Lactobacillus were enriched in L. rhamnosus-fermented soymilk. Furthermore, there was less decrease in bacterial taxa with fermented soymilk group even when antibiotics were concomitantly administered. Overall, this study revealed that the gut microbiota of a healthy host is enough for the whole isoflavone metabolism under normal conditions. Feeding mice with L. rhamnosus-fermented soymilk improved fecal enzyme activity and kept the balance of the gut mirobiota when antibiotics were used. PRACTICAL APPLICATION: Feeding mice with L. rhamnosus-fermented soymilk improved fecal enzyme activity and kept the balance of the gut mirobiota when antibiotics were used.

Feeding Pasteurized Waste Milk to Preweaned Dairy Calves Changes Fecal and Upper Respiratory Tract Microbiota.

In the present study bacterial communities from both, the gastrointestinal and respiratory tract of pre-weaned dairy calves fed two different milk-feeding programs were characterized using 16S rRNA gene sequencing. Twenty female Holstein calves (38.8 ± 1.40 kg of BW) were fed pasteurized waste milk (pWM) containing residues of various antimicrobials. Twenty additional calves (38.1 ± 1.19 kg of BW) were fed milk replacer (MR) with similar nutrient composition (27.5% crude protein, 32.1% fat) compared to waste milk (28.6% crude protein, 30.0% fat) from day 1 to weaning at day 49 of study. Fecal samples and nasal swabs were collected on day 42 only from calves that were not treated with therapeutic antibiotics throughout the study, which were 8 MR and 10 pWM calves. To assess the impact of the two feeding regimes on the fecal and nasal microbiota, α and β-diversity measures were calculated, and the relative abundance of operational taxonomic units (OTUs) at different taxonomic levels was determined for each sample. In general, Chao1, PD Whole Tree, and Shannon diversity indices were similar for the fecal and nasal bacterial communities of calves regardless of the feeding regime. However, principal coordinate analysis based on unweighted Unifrac distances indicated differences in the structure of bacterial communities of calves fed milk replacer compared with those from calves fed pasteurized waste milk. The relative abundance of the Streptococcaceae family and the genus Histophilus was greater (P < 0.05) in the nasal microbiota of calves fed milk replacer than in those fed pasteurized waste milk. However, the genus Prevotella tended (P = 0.06) to be more relatively abundant in the respiratory tract of calves fed pasteurized waste milk than in those fed milk replacer. Differences in relative abundances of bacterial taxa in gut microbiota were only observed at the phylum level, suggesting that antimicrobial residues present in waste milk have a non-specific influence at a lower taxonomical level.

The Microbiome in Functional Gastrointestinal Disorders Is Characterized by Bacteria and Genes Involved in Carbohydrate and Bile Acid Metabolism (OR23-01-19)

ObjectivesIrritable Bowel Syndrome (IBS) is a functional gastrointestinal (GI) disorder featuring chronic or recurrent abdominal discomfort, usually with changes in GI habit. To improve our understanding of links between the microbiome and IBS, and how these links can be manipulated through diet, we undertook shotgun metagenomic sequencing of fecal samples from a case-control study. MethodsFecal samples from 172 individuals were analyzed by shotgun sequencing using the Illumina NextSeq platform. Of these, 77 were classified as controls, 16 were constipation-predominant IBS (IBS-C), 39 were diarrhea-predominant IBS (IBS-D), 29 were diagnosed with functional constipation (FC), and 11 had functional diarrhea (FD). Taxonomic classifications were determined using Metaxa2 and the SILVA 128 database. Gene functions were assigned by alignment of sequences against a protein reference database using DIAMOND. Mean relative abundance of bacterial taxa and functional genes were compared using permutation ANOVA. Ethical approval was obtained from the University of Otago Human Ethics Committee (Health) (Reference H16/094). ResultsBacterial genera that discriminated case-controls (P < 0.05) from those with constipation (IBS-C + FC) and diarrhea (IBS-D + FD) included Megasphaera (increased in those with constipation), Blautia (increased in those with diarrhea), and Bilophila (increased in both constipation and diarrhea groups). Megasphaera and Blautia include bacteria that are bile-resistant and produce butyrate, possessing a wide range of Carbohydrate-Active enzymes. Bilophila are sulfite-reducing bacteria that are able to utilize bile-acids. Associated with these taxonomic differences, a wide range of genes involved in carbohydrate, energy, and amino acid metabolism differed significantly (P < 0.05), including some involved in taurine and glycine metabolism. Bile acids are conjugated with taurine or glycine in the liver, and these amino acids are removed by the action of members of the GI microbiota. ConclusionsResults from our study suggest carbohydrate and bile acid metabolism by the GI microbiome may be important distinguishing characteristics in functional GI disorders. Funding SourcesFunded by the New Zealand National Science Challenge High-Value Nutrition program.

Novel metabolome and breath platforms to trace microbiome contribution to host metabolism

Host diet influences the structure and function of the microbiota in species that regularly consume food. To measure the functional contribution of microbiotas, we developed a metabolome‐microbiome platform (MMP) and novel stable isotopic labeling to trace microbiotas' metabolism in breath, cecum, and host tissues. We combined cavity ringdown spectroscopy to measure real‐time breath biomarkers and NMR‐based metabolomics to analyze metabolome profiles in tissues. We applied MMP to hibernating ground squirrels to assess the role of bacterial metabolism contributing to seasonal changes in diet. Previously, we showed that the long‐term fast of hibernation decreases relative abundance of bacterial taxa that are adept at degrading abundant plant glycans in summer versus their reduction in winter. Here, we determined the functional significance of seasonally changing microbiotas by gavaging Spring and Summer squirrels and aroused hibernators in Winter with 13C‐labeled complex and simple carbohydrates, and comparing against their respective intraperitoneal and antibiotics applications. Measurement of 13CO2/12CO2(δ13C) in breath was used as an index of bacterial degradation of 13C‐substrates and linked to observed changes in 1H‐[13C]‐metabolome profiles. Compared with robust responses in Summer changes in δ13C after 13C‐inulin gavage in hibernators were nearly abolished, whereas squirrels in Early Winter and Spring showed variable responses consistent with their transitional microbiotas. Metabolome profiles mirrored seasonal changes in 13C‐labeled short‐chain fatty acids. These suggest that during hibernation, the gut microbiota gradually loses the capacity to degrade a plant‐derived glycan, and a shift away from taxa that prefer dietary substrates. The results suggest MMP is a powerful tool in analysis of host‐microbe relationships.Support or Funding InformationSupported by funds from NSF (IOS1558044), UW‐Madison Graduate and Veterinary Medicine.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity

Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks (“blue carbon”). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.

Comparison of the Vaginal Microbiomes of Premenopausal and Postmenopausal Women.

For decades hormone therapy (HT) has been prescribed to treat the symptoms of menopause, such as vaginal dryness, itching and burning. Here we sought to compare the vaginal microbiomes of postmenopausal women who received low dose estrogen therapy to those of premenopausal and postmenopausal women, and to do so in conjunction with assessing the alleviation of symptoms associated with vaginal atrophy. In this study vaginal swab samples were obtained from 45 women who were classified as either premenopausal, postmenopausal, or postmenopausal and undergoing HT. The vaginal microbiomes of these women were characterized by 16S rRNA gene sequencing and bacterial abundances were quantified by qPCR. We found that the vaginal communities from our cohort could be divided into six clusters (A-F) based on differences in the composition and relative abundances of bacterial taxa. Communities in cluster A were dominated by Lactobacillus crispatus, and those of cluster B were dominated by Gardnerella vaginalis. Communities in cluster C had high proportions of L. iners, while those in cluster D were more even and included several co-dominant taxa. Communities in clusters E and F were dominated by Bifidobacterium and L. gasseri, respectively. The vaginal communities of most postmenopausal women receiving HT (10/15) were dominated by species of lactobacilli and belonged to clusters A, C, and F (P < 0.001). This sharply contrasts with vaginal communities of postmenopausal women without HT, most of which (10/15) were in cluster D, depleted of lactobacilli, and had about 10-fold fewer total bacteria (P < 0.05). The vaginal communities of women in each study group differed in terms of the dominant bacterial species composition and relative abundance. Those of postmenopausal women receiving HT significantly differed from those of postmenopausal women without HT and were most often dominated by species of Lactobacillus. Noteworthy, HT greatly improved vaginal atrophy scores, decreased vaginal pH, and significantly increased bacterial numbers in comparison to postmenopausal women not receiving HT.

Association of Systemic Antibiotic Treatment of Acne With Skin Microbiota Characteristics

Given the widespread use of systemic antibiotics for treatment of moderate to severe acne, it is important to understand the associations of such antibiotic use with changes not only in Cutibacterium acnes (formerly Propionibacterium acnes) but also in the complete bacterial community of the skin. To examine the composition, diversity, and resilience of skin microbiota associated with systemic antibiotic perturbation in individuals with acne. This longitudinal cohort study conducted at an academic referral center in Maryland from February 11 to September 23, 2014, included 4 female participants who had received a recent diagnosis of acne vulgaris, showed comedonal and inflammatory acne on the face, were at least 18 years old, and had no recent use of systemic or topical treatments for acne, including antibiotics and retinoids. Data analysis was performed between July 5, 2017, and November 7, 2018. Participants were prescribed oral minocycline, 100 mg, twice daily for 4 weeks. Skin areas on the forehead, cheek, and chin were sampled for 16S ribosomal RNA gene sequencing at baseline, 4 weeks after starting minocycline treatment, and then 1 week and 8 weeks after discontinuation of treatment. Skin microbiota examined with respect to relative abundance of bacterial taxa, α diversity (represents within-sample microbial diversity), and β diversity (represents between-sample microbial diversity). Acne status evaluated with photography and lesion count. Of the 4 patients included in this study, 2 were 25 years old, 1 was 29 years old, and 1 was 35 years old; 2 were white women, 1 was an African American woman, and 1 was an Asian woman. Across all 4 patients, antibiotic treatment was associated with a 1.4-fold reduction in the level of C acnes (difference, -10.3%; 95% CI, -19.9% to -0.7%; P = .04) with recovery following cessation of treatment. Distinct patterns of change were identified in multiple bacterial genera, including a transient 5.6-fold increase in the relative abundance of Pseudomonas species (difference, 2.2%; 95% CI, 0.9%-3.4%; P < .001) immediately following antibiotic treatment, as well as a persistent 1.7-fold increase in the relative abundance of Streptococcus species (difference, 5.4%; 95% CI, 0.3%-10.6%; P = .04) and a 4.7-fold decrease in the relative abundance of Lactobacillus species (difference, -0.8%; 95% CI, -1.4% to -0.2%; P = .02) 8 weeks following antibiotic treatment withdrawal. In general, antibiotic administration was associated with an initial decrease from baseline of bacterial diversity followed by recovery. Principal coordinates analysis results showed moderate clustering of samples by patient (analysis of similarity, R = 0.424; P = .001) and significant clustering of samples by time in one participant (analysis of similarity, R = 0.733; P = .001). In this study, systemic antibiotic treatment of acne was associated with changes in the composition and diversity of skin microbiota, with variable rates of recovery across individual patients and parallel changes in specific bacterial populations. Understanding the association between systemic antibiotic use and skin microbiota may help clinicians decrease the likelihood of skin comorbidities related to microbial dysbiosis.

1773. Impact of Antibiotics Used to Treat Community Acquired Pneumonia on the Gut Microbiome and Resistome in Healthy Volunteers

BackgroundAntibiotics (ABX) are frequently inappropriately used to treat nonbacterial causes of respiratory illnesses. The goal of this prospective cohort study was to characterize the impact of ABX used to treat community-acquired pneumonia (CAP) on the fecal microbiome and resistome in healthy volunteers (HV).MethodsTwenty HVs were randomized to receive 5 days of levofloxacin (LV), azithromycin (AZ), cefpodoxime (CF), or AZ+CF. Stool was collected before, during, and after ABX, then underwent microbiologic culture and shotgun sequencing. DNA was extracted, then sequenced using the Illumina NextSeq platform. Relative abundance of bacterial taxa was estimated by MetaPhlAn and antibiotic resistance gene (ARG) composition by ShortBRED. Analysis was in R.ResultsThe mean HV age was 37 (range 24–59) and 10 were female. Species diversity measured via Shannon Index and richness were significantly lower in samples taken from all HVs 3 days post-ABX (P < 0.01 for all). While nonmetric multidimensional scaling (NDMS) ordination shows high interpatient dissimilarity (Bray–Curtis) for most samples, the post-ABX intrapatient dissimilarity varies by ABX. The AZ group exhibited chronic alterations in taxa dissimilarity and the CF group had increases in dissimilarity directly post-ABX. The CF+AZ group displayed both acute and persistent perturbations (Figure 1). Although there was no significant change in ARG richness post-ABX, there was a significant increase in overall ARG abundance across all samples (P < 0.003). Within each ABX, there were unique changes in ARG abundance, and groups with CF had increases in ARG abundance (Figure 2).ConclusionABX used to treat CAP can cause acute microbiome disruptions, as evidenced by decreased microbiome species diversity and richness, and an increase in ARG abundance post-ABX. The duration of this impact is variable. To prevent microbiome disruptions, measures to prevent inappropriate ABX use via ABX stewardship are necessary. Disclosures E. R. Dubberke, Rebiotix: Consultant and Investigator, Consulting fee and Research support. Pfizer: Consultant and Grant Investigator, Consulting fee and Research grant. Synthetic biologics: Consultant, Consulting fee. Merck: Consultant and Investigator, Consulting fee and Research support. Valneva: Consultant, Consulting fee. Achaogen: Consultant, Consulting fee. Alere: webinar, Speaker honorarium. Biofire: webinar, Speaker honorarium.

Altered Gut Microbiota in Myasthenia Gravis.

Myasthenia gravis (MG) is an autoimmune-mediated disorder, the etiology of which involves both environmental factors and genetics. While the exact factors responsible for predisposition to MG remain elusive, it is hypothesized that gut microbiota play a critical role in the pathogenesis of MG. This study investigated whether gut microbiota are altered in MG patients by comparing the fecal microbiota profiles of MG patients to those of age- and sex-matched healthy controls. Phylotype profiles of gut microbial populations were generated using hypervariable tag sequencing of the V4 region of the 16S ribosomal RNA gene. Fecal short-chain fatty acids (SCFAs) were assessed by gas chromatographic analyses. The results demonstrated that, compared to the healthy cohort, the gut microbiota of the MG group was changed in terms of the relative abundances of bacterial taxa, with sharply reduced microbial richness, particularly in the genus Clostridium. The fecal SCFA content was significantly lower in the MG group. Furthermore, microbial dysbiosis was closely related to the levels of inflammatory biomarkers in the sera of MG patients.

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia.

Ocean warming is known to cause detrimental effects in coral reef fauna that rely on photo-symbiosis for survival. Microbial associations can facilitate the success of species across a range of environmental conditions, and play a role in the capacity of organisms to respond to climate change. In 2016, the Great Barrier Reef experienced its third mass bleaching event, with sea surface temperature rising to 1.3°C above long-term monthly summer averages. Here, I investigate the effects of ocean warming on the chlorophyll a (chl a) content and microbiome of the large benthic Foraminifera Amphistegina radiata. Samples were collected in January and April 2016, before and after the mass bleaching event. In total, 71 specimens were collected from two different depths (6- and 18-m) to investigate depth-dependant responses associated with changes in chl a and microbiome. Pigment analysis showed a significant reduction in chl a between time points in specimens collected at both depths. Reduction in pigmentation was accompanied by changes in the microbiome, and a significant interaction of depth and time was observed. Genus-level bacterial community associated with A. radiata was significantly different across depth and time. However, ocean warming affected populations at both depths to a similar extent, and resulted in change from a Betaproteobacteria-dominated assemblage in January to a more diverse bacterial community by April. Analysis of presence/absence and relative abundance of bacterial taxa revealed significant differences between time points at both depths analyzed. OTUs classified as Firmicutes, which were either absent, or present in very low relative abundances (<0.1%) across all sample groups in January, were identified in abundances as high as ∼20% in specimens collected from 18-m depth in April. Class-level shifts were observed in shallow-dwelling specimens, from high abundances of Betaproteobacteria to a high abundance and diversity of Actinobacteria. These results demonstrate the sensitivity of LBF to the effects of ocean warming, for which depth did not provide protection, and highlights the capacity of LBF to re-assemble bacterial communities after a disturbance. This study provides the first molecular-based demonstration of changes in foraminifera-associated bacterial assemblages during a bleaching event on a natural reef system.

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.

Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes, as well as a linear response over more than 3 logs of input RNA. Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString, and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. Compared at the genus level, the relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. We propose that this method may complement other methods designed to understand dynamic microbial communities, may provide information on bacteria and fungi in the same sample with a single assay, and with further development, may provide quick and easily interpreted diagnostic information on diverse bacteria and fungi at the genus or species level.IMPORTANCE Here we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host response to changes in microbial communities.

The impact of epidermal growth factor supernatant on pig performance and ileal microbiota.

Weaning of pigs can lead to low-feed intake resulting in a lag in growth performance, reduced gut health, and diarrheal diseases. Epidermal growth factor (EGF), the most abundant growth factor in milk, increased weaned pig BW gain and feed efficiency in our previous work. It is believed that intestinal microbiota plays an important role in gut health and pig growth, but limited data are available on the impact of feed additives, such as EGF, on the microbial communities of the intestines. The objective of the study was to investigate if the positive influence of EGF supplementation on weight gain and gut health was related to differences in intestinal microbiota. To examine the efficacy of EGF, a 21-d animal trial was performed using 72 pigs (two equal blocks of 36 pigs with three barrows and three gilts/pen). Pigs were assigned to one of two dietary treatments at weaning (20 ± 2 d of age; n = 6 pens/treatment) balancing across treatment for litter, gender, and initial BW. Recombinant yeast supernatant containing EGF at 120 μg/kg BW/d and without EGF (control) was added to the feed for 21 d, followed by a common diet for 7 d. Pig performance was measured weekly and ileal digesta was collected at day 21 from six pigs/treatment for microbiome analysis. Pigs fed diets containing EGF fermentation supernatant had greater (P = 0.01) daily gain in week 3 and overall resulting in heavier (P = 0.029) BW at day 28, which was consistent to our previous finding. No difference in alpha-diversity (Chao1, Shanon, and Simpson indices) and beta-diversity (weighted and unweighted UniFrac distances) of ileal digesta microbiota between EGF supplemented and control pigs were observed. The relative abundances of bacterial taxa did not differ among treatment groups at the phylum level. The relative abundances of Corynebacterium (0.0 vs. 0.9%), Blautia (0.003 vs. 0.26%), and Coprococcus (0.0 vs. 0.05%) genera, and Rumminococcaceae family (0.001 vs. 0.08%) were decreased (P < 0.05) in EGF group compared to control and were negatively correlated (P < 0.05, r > 0.60) with growth performance. Pathways related to detoxification and carbohydrate metabolism were differentially represented in the luminal bacterial populations. The improved growth of pigs supplemented with EGF supernatant produced by Pichia pastoris may be related to changes in functional capacity of the gut microbial populations. However, the impact on mucosa-associated or large intestinal communities is still unknown.

Variation in Bat Guano Bacterial Community Composition With Depth.

Bats are known to be reservoirs for a variety of mammalian pathogens, including viruses, fungi, and bacteria. Many of the studies examining the microbial community inhabiting bats have investigated bacterial taxa found within specific bat tissues and isolated bat guano pellets, but relatively few studies have explored bacterial diversity within bat guano piles. In large bat caves, bat guano can accumulate over time, creating piles several meters deep and forming complex interactions with coprophagous organisms in a habitat with low light and oxygen. As the guano decays, the nutrient composition changes, but the bacterial communities deep within the pile have not been characterized. Here, we assess the bacterial communities across varying depths within the guano pile using both culture-independent and culture-dependent methods. We found that although similar taxa are found throughout the guano pile, the relative abundances of taxa within the pile shift, allowing certain taxa to dominate the bacterial community at varying depths. We also identified potential bacterial functions being performed within the bat guano as various depths within the pile and found little variation in terms of the dominant predicted functions, suggesting that although the relative abundances of bacterial taxa are changing, the functions being performed are similar. Additionally, we cultured 15 different bacterial species, including 2 not present in our culture-independent analysis, and discuss the pathogenicity potential of these taxa. This study represents the first characterization of the bacterial community from the extreme environment within a bat guano pile and demonstrates the potential for bat caves as resources for identifying new bacterial species.

Predicting Hydrologic Function With Aquatic Gene Fragments

AbstractRecent advances in microbiology techniques, such as genetic sequencing, allow for rapid and cost‐effective collection of large quantities of genetic information carried within water samples. Here we posit that the unique composition of aquatic DNA material within a water sample contains relevant information about hydrologic function at multiple temporal scales. In this study, machine learning was used to develop discharge prediction models trained on the relative abundance of bacterial taxa classified into operational taxonomic units (OTUs) based on 16S rRNA gene sequences from six large arctic rivers. We term this approach “genohydrology,” and show that OTU relative abundances can be used to predict river discharge at monthly and longer timescales. Based on a single DNA sample from each river, the average Nash‐Sutcliffe efficiency (NSE) for predicted mean monthly discharge values throughout the year was 0.84, while the NSE for predicted discharge values across different return intervals was 0.67. These are considerable improvements over predictions based only on the area‐scaled mean specific discharge of five similar rivers, which had average NSE values of 0.64 and −0.32 for seasonal and recurrence interval discharge values, respectively. The genohydrology approach demonstrates that genetic diversity within the aquatic microbiome is a large and underutilized data resource with benefits for prediction of hydrologic function.

Abstract P1-05-01: Breast cancer and the human microbiome

Abstract The human body harbors ten times more bacterial cells than human cells – a stunning figure that suggests a likely dynamic between our bodies and the bacteria we carry, both in health and disease. In this study, we characterized and compared the gut, oral, and breast tissue microbiomes from women with invasive breast cancer, women with ductal carcinoma in situ (DCIS), and healthy women. Samples were collected prior to any systemic therapy to avoid therapy-associated effects on the microbiomes studied. Kits containing materials for collecting oral and stool swab samples were distributed to patients for self-collection. DNA was isolated from these samples and bacterial 16S rRNA was PCR amplified and sequenced. Based on the sequencing results, bacterial taxa present in the samples were enumerated. In our analyses, we looked at microbial diversity and differential relative abundance of bacterial taxa across the three cohorts. Oral and gut microbial diversity at various taxa levels were assessed using Shannon and Simpson diversity indices. The oral microbiome did not show any significant difference in microbial diversity across the three cohorts. In the gut microbiome, the invasive cohort showed a significant decrease in microbial diversity when compared to the healthy cohort. Differences in phylogenetic and relative abundance of bacterial taxa across the three cohorts were measured using a T-test analysis with a p value less than 0.05 considered significant. In the oral microbiome, there were no significant differences in the relative abundance of bacteria across the three cohorts. In the gut microbiome, there were significant differences in the relative abundance of bacteria within each cohort on the phylum, family, and genus levels. The genus Fusicanterbacter (associated with the Lachnospiracaea family and Firmicutes phylum) was significantly overabundant in gut microbiomes of healthy women when compared to the gut microbiomes of women with DCIS or invasive breast cancer. Meanwhile, the genus Bacteriodes (associated with the Bacteroidaceae family and Bacteriodetes phylum) was significantly overabundant in the gut microbiomes of women with invasive breast cancer when compared to the gut microbiomes of healthy women. Although tissues are often thought of as sterile, there is emerging data indicating that different tissues may harbor their own unique microbiomes. We obtained breast tissue microbiome data from a small subset of our breast cancer and DCIS cohorts, as well as healthy breast tissue from reduction mammaplasty specimens. At the genus level, we observed an enrichment of Lactococcus, Lactobacillus, and Halomonas in healthy breast tissues compared to breast cancer tissues and an enrichment of Hyphomicrobium in breast cancer tissues compared to healthy breast tissues. Understanding how gut, oral, and tissue microbiomes relate to breast cancer may open up new opportunities for the development of novel markers for early detection (or markers of susceptibility) as well as new strategies for prevention and/or treatment. Citation Format: McCune E, Johnson B, O'Meara T, Theiner S, Campos M, Heditsian D, Brain S, Esserman L, Campbell M. Breast cancer and the human microbiome [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-05-01.