Gut microbiota composition is associated with narcolepsy type 1

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock

Scientific Reports ◽

10.1038/s41598-021-85897-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sandra A. Appiah ◽

Christine L. Foxx ◽

Dominik Langgartner ◽

Annette Palmer ◽

Cristian A. Zambrano ◽

...

Keyword(s):

Gut Microbiota ◽

Community Composition ◽

Gut Microbiome ◽

Beta Diversity ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Global Changes ◽

Rrna Gene ◽

Alpha And Beta Diversity ◽

Increased Risk

AbstractSevere injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.

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Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome

PLoS ONE ◽

10.1371/journal.pone.0248030 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248030

Author(s):

Heidi M. L. Wipf ◽

Devin Coleman-Derr

Keyword(s):

Ploidy Level ◽

Bacterial Communities ◽

Beta Diversity ◽

Driving Forces ◽

Amplicon Sequencing ◽

P Value ◽

Rrna Gene ◽

Crop Species ◽

Wheat Varieties ◽

Alpha And Beta Diversity

While numerous studies implicate the microbiome in host fitness, contributions of host evolution to microbial recruitment remain largely uncharacterized. Past work has shown that plant polyploidy and domestication can influence plant biotic and abiotic interactions, yet impacts on broader microbiome assembly are still unknown for many crop species. In this study, we utilized three approaches—two field studies and one greenhouse-based experiment—to determine the degree to which patterns in bacterial community assembly in wheat (Triticum sp.) roots and rhizospheres are attributable to the host factors of ploidy level (2n, 4n, 6n) and domestication status (cultivated vs. wild). Profiling belowground bacterial communities with 16S rRNA gene amplicon sequencing, we analyzed patterns in diversity and composition. From our initial analyses of a subsetted dataset, we observed that host ploidy level was statistically significant in explaining variation in alpha and beta diversity for rhizosphere microbiomes, as well as correlated with distinct phylum-level shifts in composition, in the field. Using a reduced complexity field soil inoculum and controlled greenhouse conditions, we found some evidence suggesting that genomic lineage and ploidy level influence root alpha and beta diversity (p-value<0.05). However, in a follow-up field experiment using an expanded set of Triticum genomes that included both wild and domesticated varieties, we did not find a strong signal for either diploid genome lineages, domestication status, or ploidy level in shaping rhizosphere bacterial communities. Taken together, these results suggest that while host ploidy and domestication may have some minor influence on microbial assembly, these impacts are subtle and difficult to assess in belowground compartments for wheat varieties. By improving our understanding of the degree to which host ploidy and cultivation factors shape the plant microbiome, this research informs perspectives on what key driving forces may underlie microbiome structuring, as well as where future efforts may be best directed towards fortifying plant growth by microbial means. The greatest influence of the host on the wheat microbiome appeared to occur in the rhizosphere compartment, and we suggest that future work focuses on this environment to further characterize how host genomic and phenotypic changes influence plant-microbe communications.

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Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

Current Developments in Nutrition ◽

10.1093/cdn/nzab027 ◽

2021 ◽

Author(s):

Maciej Chichlowski ◽

Nicholas Bokulich ◽

Cheryl L Harris ◽

Jennifer L Wampler ◽

Fei Li ◽

...

Keyword(s):

Infant Formula ◽

Beta Diversity ◽

Milk Fat ◽

Alpha Diversity ◽

Illumina Miseq ◽

Rrna Gene ◽

Term Infants ◽

Linear Discriminant ◽

Alpha And Beta Diversity ◽

Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration: https://clinicaltrials.gov/ct2/show/NCT02274883).

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AB1232 ORAL DYSBIOSIS REFLECTS THE IMMUNOLOGICAL ALTERATION OF RA REGARDING TO ACPA AND HLA DRB1*SE: NAGASAKI ISLAND STUDY

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-eular.5147 ◽

2020 ◽

Vol 79 (Suppl 1) ◽

pp. 1907.2-1907

Author(s):

Y. Tsuji ◽

M. Tamai ◽

S. Morimoto ◽

D. Sasaki ◽

M. Nagayoshi ◽

...

Keyword(s):

Beta Diversity ◽

Healthy Subjects ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Enzyme Linked Immunosorbent Assay ◽

Rrna Gene ◽

Oral Microbiota ◽

Unifrac Distance ◽

Alpha And Beta Diversity ◽

The Difference

Background:Anti-citrullinated protein antibody (ACPA) production is observed in several organs even prior to the onset of rheumatoid arthritis (RA), and oral mucosa is considered to be one of the important tissues. The presence of HLA-DRB1*SE closely associates with ACPA production. Saliva is considered to reflect the oral microbiota including periodontal disease. Alteration of oral microbiota of RA becomes to be normalized by DMARDs treatment, however, the interaction of HLA-DRB1*SE, ACPA and oral microbiota of RA patients remains to be elucidated.Objectives:The Nagasaki Island Study, which had started in 2014 collaborating with Goto City, is intended for research of the preclinical stage of RA, including ACPA/HLA genotype screening and ultrasound and magnetic resonance imaging examinations in high-risk subjects. Using the samples accumulated in this cohort, we have tried to investigate the difference of oral microbiota among RA patients and healthy subjects regarding to ACPA and HLA-DRB1*SE.Methods:Blood and salivary samples were obtained from 1422 subjects out of 4276 who have participated in the Nagasaki Island Study from 2016 to 2018. ACPA positivity was 1.7 % in total. Some of RA patients resided in Goto City participated in the Nagasaki Island Study. At this point, we selected 291 subjects, who were ACPA positive non-RA healthy subjects (n=22) and patients with RA (n=33, 11 subjects were ACPA positive and 22 ACPA negative respectively) as the case, age and gender matched ACPA negative non-RA healthy subjects (n=236) as the control. ACPA was measured by an enzyme-linked immunosorbent assay, and HLA genotyping was quantified by next-generation sequencing (Ref.1). The operational taxonomic unit (OUT) analysis using 16S rRNA gene sequencing were performed. The richness of microbial diversity within-subject (alpha diversity) was scaled via Shannon entropy. The dissimilarity between microbial community composition was calculated using Bray-Curtis distance as a scale, and differences between groups (beta diversity) were tested by permutational multivariate analysis of variance (PERMANOVA). In addition, UniFrac distance calculated in consideration of the distance on the phylogenetic tree were performed.Results:Median age 70 y.o., % Female 58.8 %. Among RA and non-RA subjects, not alpha diversity but beta diversity was statistically significance (p=0.022, small in RA). In RA subjects, both alpha and beta diversity is small (p<0.0001), especially significant in ACPA positive RA (Figure 1). Amongt RA subjects, presence of HLA-DRB1*SE did not show the difference but the tendency of being small of alpha diversity (p=0.29).Conclusion:Our study has suggested for the first time the association of oral microbiota alteration with the presence of ACPA and HLA-DRB1*SE. Oral dysbiosis may reflect the immunological status of patients with RA.References:[1]Kawaguchi S, et al. Methods Mol Biol 2018;1802: 22Disclosure of Interests:None declared

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Gut bacterial microbiota in patients with myasthenia gravis: results from the MYBIOM study

Therapeutic Advances in Neurological Disorders ◽

10.1177/17562864211035657 ◽

2021 ◽

Vol 14 ◽

pp. 175628642110356

Author(s):

Andreas Totzeck ◽

Elakiya Ramakrishnan ◽

Melina Schlag ◽

Benjamin Stolte ◽

Kathrin Kizina ◽

...

Keyword(s):

Gut Microbiota ◽

Myasthenia Gravis ◽

Healthy Volunteers ◽

Alpha Diversity ◽

Diversity Indices ◽

Rrna Gene ◽

Pilot Studies ◽

Variable Regions ◽

Alpha And Beta Diversity ◽

Significant Difference

Background: Myasthenia gravis (MG) is an autoimmune neuromuscular disease, with gut microbiota considered to be a pathogenetic factor. Previous pilot studies have found differences in the gut microbiota of patients with MG and healthy individuals. To determine whether gut microbiota has a pathogenetic role in MG, we compared the gut microbiota of patients with MG with that of patients with non-inflammatory and inflammatory neurological disorders of the peripheral nervous system (primary endpoint) and healthy volunteers (secondary endpoint). Methods: Faecal samples were collected from patients with MG ( n = 41), non-inflammatory neurological disorder (NIND, n = 18), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 6) and healthy volunteers ( n = 12). DNA was isolated from these samples, and the variable regions of the 16S rRNA gene were sequenced and statistically analysed. Results: No differences were found in alpha- and beta-diversity indices computed between the MG, NIND and CIDP groups, indicating an unaltered bacterial diversity and structure of the microbial community. However, the alpha-diversity indices, namely Shannon, Chao 1 and abundance-based coverage estimators, were significantly reduced between the MG group and healthy volunteers. Deltaproteobacteria and Faecalibacterium were abundant within the faecal microbiota of patients with MG compared with controls with non-inflammatory diseases. Conclusion: Although the overall diversity and structure of the gut microbiota did not differ between the MG, NIND and CIDP groups, the significant difference in the abundance of Deltaproteobacteria and Faecalibacterium supports the possible role of gut microbiota as a contributor to pathogenesis of MG. Further studies are needed to confirm these findings and to develop possible treatment strategies.

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PSVI-16 Fecal microbiome of nursery pigs fed phytogenics and antibiotics

Journal of Animal Science ◽

10.1093/jas/skz258.418 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 203-203

Author(s):

Huyen Tran ◽

Timothy J Johnson

Keyword(s):

Beta Diversity ◽

Sequence Data ◽

Alpha Diversity ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Fecal Microbiome ◽

Nursery Pigs ◽

Alpha And Beta Diversity ◽

Family Level ◽

Dietary Treatments

Abstract The objective of this study was to evaluate effects of feeding two phytogenic products (PHY1 and PHY2; blends of essential oils and plant extracts) in diets with or without antibiotics (AureoMix S 10-10; AB) on fecal microbiome of nursery pigs. A total of 400 nursery pigs (6.8 kg BW; 20 d of age) were fed one of the six dietary treatments (9 pens/treatment), including: control (0% AB; 0% phytogenics), 0.5% AB, phytogenics (0.02% PHY1 or 0.03% PHY2) or the combination of phytogenic and AB (PHY1 x AB or PHY2 x AB). On d 46 postweaning, 48 fecal samples were collected (1 pig/pen; 7–9 pigs/treatment) and were subjected to the analyses of microbial communities by using 16S rRNA V4 amplicon sequencing with Illumina MiSeq. The sequence data were analyzed by using Qiime and the rarefied OTU table was submitted to Calypso to evaluate the alpha and beta diversity, taxonomic classification, and the differential taxa associated to the dietary treatments. There were differences among treatments on alpha diversity, where the control and PHY2 pigs had lower OTU richness (P = 0.05) and chao1 index (P < 0.10) compared to pigs fed AB alone or AB with phytogenics. There were also differences among treatments on microbial beta diversity of pigs (P < 0.01). The most abundant phyla included Firmicute, Bacteroidetes, Actinobacteria, Tenericutes, Proteobacteria, Spirochaetes, and TM7. At family level, pigs fed AB had greater Ruminococcaceae compared to the control, but lower Coriobacteriaceae and Erysipelotrichaceae compared to PHY1 or PHY2 group (P < 0.05). Feature selection by LEfSe indicated that dominant genus associated to AB treatment was Unclassified RF39, while dominant genera associated to PHY2 treatment were Cantenibacterium, unclassified Coriobacteriaceae, Blautia, Eubacterium, and Collinsella. In conclusion, feeding AB and phytogenic products had different impacts on the fecal bacteria of nursery pigs.

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Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz179 ◽

2019 ◽

Author(s):

Lara Parata ◽

Shaun Nielsen ◽

Xing Xing ◽

Torsten Thomas ◽

Suhelen Egan ◽

...

Keyword(s):

Coral Reef ◽

Gastrointestinal Tract ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Communities ◽

Food Source ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Bacterial Symbionts ◽

Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

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Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors

10.1101/2020.10.15.341966 ◽

2020 ◽

Author(s):

Ezequiel Santillan ◽

Hari Seshan ◽

Stefan Wuertz

Keyword(s):

Community Structure ◽

Bacterial Communities ◽

Temporal Dynamics ◽

Treatment Plant ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Batch Reactors ◽

Function Structure ◽

Community Function ◽

And Function

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract

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Human Milk Feeding Patterns at 6 Months of Age are a Major Determinant of Fecal Bacterial Diversity in Infants

Journal of Human Lactation ◽

10.1177/0890334420957571 ◽

2020 ◽

pp. 089033442095757

Author(s):

Kameron Y. Sugino ◽

Tengfei Ma ◽

Jean M. Kerver ◽

Nigel Paneth ◽

Sarah S. Comstock

Keyword(s):

Gut Microbiota ◽

Human Milk ◽

Beta Diversity ◽

Maternal Obesity ◽

Alpha Diversity ◽

Major Determinant ◽

Cross Sectional ◽

Alpha And Beta Diversity ◽

Infant Diet ◽

Milk Feeding

Background Maternal pre-pregnancy obesity and human milk feeding have been associated with altered infant gut microbiota. Research aim Determine the relationships between maternal pre-pregnancy BMI, human milk exposure, and their influence on the infant microbiota simultaneously. Methods This was a cross-sectional study of infants at 6 months of age ( N = 36), a time when many infants are fed a mixed diet of human milk and other foods. Fecal samples and participant information were collected from a subset of dyads enrolled in two related prospective cohorts (ARCHGUT and BABYGUT) in Michigan. Sequencing the V4 region of the 16S gene was used to analyze fecal bacterial samples collected from 6-month-old infants. Participants were grouped into four categories designated by their extent of human milk exposure (100%, 80%, 50%–80%, ≤ 20% human milk in the infant diet) and by maternal pre-pregnancy BMI category (normal, overweight, obese). Results Fewer participants with pre-pregnancy obesity were breastfeeding at 6 months postpartum compared to non-obese participants (35.7% and 81.8%, respectively). In univariate analyses, maternal pre-pregnancy BMI and human milk exposure were both significantly associated with alpha and beta diversity of the infant microbiota. However, in multivariate analyses, human milk exposure accounted for 20% of the variation in alpha diversity, but pre-pregnancy BMI was not significantly associated with any form of microbiota diversity. Conclusions The proportion of the infant diet that was human milk at 6 months was the major determinant of alpha and beta diversity of the infant. Maternal obesity contributes to the gut microbiota by its association with the extent of human milk feeding.

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Inconsistent Patterns of Microbial Diversity and Composition Between Highly Similar Sequencing Protocols: A Case Study With Reef-Building Corals

Frontiers in Microbiology ◽

10.3389/fmicb.2021.740932 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hannah E. Epstein ◽

Alejandra Hernandez-Agreda ◽

Samuel Starko ◽

Julia K. Baum ◽

Rebecca Vega Thurber

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Beta Diversity ◽

Sequence Data ◽

Alpha Diversity ◽

Gene Profiling ◽

Rrna Gene ◽

Sequencing Platform ◽

Alpha And Beta Diversity ◽

Diversity Metrics

16S rRNA gene profiling (amplicon sequencing) is a popular technique for understanding host-associated and environmental microbial communities. Most protocols for sequencing amplicon libraries follow a standardized pipeline that can differ slightly depending on laboratory facility and user. Given that the same variable region of the 16S gene is targeted, it is generally accepted that sequencing output from differing protocols are comparable and this assumption underlies our ability to identify universal patterns in microbial dynamics through meta-analyses. However, discrepant results from a combined 16S rRNA gene dataset prepared by two labs whose protocols differed only in DNA polymerase and sequencing platform led us to scrutinize the outputs and challenge the idea of confidently combining them for standard microbiome analysis. Using technical replicates of reef-building coral samples from two species, Montipora aequituberculata and Porites lobata, we evaluated the consistency of alpha and beta diversity metrics between data resulting from these highly similar protocols. While we found minimal variation in alpha diversity between platform, significant differences were revealed with most beta diversity metrics, dependent on host species. These inconsistencies persisted following removal of low abundance taxa and when comparing across higher taxonomic levels, suggesting that bacterial community differences associated with sequencing protocol are likely to be context dependent and difficult to correct without extensive validation work. The results of this study encourage caution in the statistical comparison and interpretation of studies that combine rRNA gene sequence data from distinct protocols and point to a need for further work identifying mechanistic causes of these observed differences.

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