Taxonomic Relative Abundance Research Articles

The effects of AG1® supplementation on the gut microbiome of healthy adults: a randomized, double-blind, placebo-controlled clinical trial.

This study aimed to examine the effect of a commercially available multi-ingredient powder (AG1Ⓡ) on the gut microbiome and assess the impact of AG1Ⓡ on GI tolerability and other clinical safety markers in healthy men and women. Using a double-blind, randomized, two-arm, placebo-controlled, parallel design, we examined a 4-week daily supplementation regimen of AG1Ⓡ vs. placebo (PL). Fifteen men and 15 women provided stool samples for microbiome analysis, questionnaires for digestive quality of life (DQLQ), and completed visual analog scales (VAS) and Bristol stool charts to assess stool consistency and bowel frequency before and after the 4-week intervention. Participant's blood work (CBC, CMP, and lipid panel) was also assessed before and after the 4-week intervention. Alpha diversity was determined by Shannon and Chao1 index scores and evaluated by a two-way ANOVA, beta diversity in taxonomic abundances and functional pathways was visualized using partial least squares-discriminant analyses and statistically evaluated by PERMANOVA. To identify key biomarkers, specific feature differences in taxonomic relative abundance and normalized functional pathway counts were analyzed by linear discriminant analysis (LDA) effect size (LEfSe). Questionnaires, clinical safety markers, and hemodynamics were evaluated by mixed factorial ANOVAs with repeated measures. This study was registered on clinicaltrials.gov (NCT06181214). AG1Ⓡ supplementation enriched two probiotic taxa (Lactobacillus acidophilus and Bifidobacterium bifidum) that likely stem from the probiotics species that exist in the product, as well as L. lactis CH_LC01 and Acetatifactor sp900066565 ASM1486575v1 while reducing Clostridium sp000435835. Regarding community function, AG1Ⓡ showed an enrichment of two functional pathways while diminishing none. Alternatively, the PL enriched six, but diminished five functional pathways. Neither treatment negatively impacted the digestive quality of life via DQLQ, bowel frequency via VAS, or stool consistency via VAS and Bristol. However, there may have been a greater improvement in the DQLQ score (+62.5%, p = 0.058, d = 0.73) after four weeks of AG1Ⓡ supplementation compared to a reduction (-50%) in PL. Furthermore, AG1Ⓡ did not significantly alter clinical safety markers following supplementation providing evidence for its safety profile. AG1Ⓡ can be consumed safely by healthy adults over four weeks with a potential beneficial impact in their digestive symptom quality of life.

Premodulator microbiome alterations associated with postmodulator growth outcomes in pediatric cystic fibrosis: Can we predict outcomes?

The gut microbiota plays an important role in childhood growth. Our longitudinal cohort includes children with cystic fibrosis (CwCF) treated with highly effective modulator therapy. We aimed to elucidate early premodulator microbial signatures associated with postmodulator weight for CwCF later in childhood. Stool samples were collected from CwCF at 13 days to 60 months. Metagenomic sequencing determined differentially abundant taxa. Children with body mass index or weight for length Z-scores within 1 standard deviation of the mean (SD) were considered normal weight, those >1 SD were classified as risk of overweight while children <1 SD were considered undernourished, although no CwCF met this latter criterion here. Multivariate regression models were applied to identify significant associations between metadata and microbial taxonomic relative abundances. One hundred and eighty-nine stool samples were analyzed from 39 CwCF. We identified statistically significant differences in early microbiome patterns among those at risk of being overweight compared to those who were normal weight when adjusted for age, sex, CF mutation, and early feeding method. Early microbiome was a stronger driver of growth status than current modulator use. Among those at risk of overweight, several taxa that were consistently in lower abundance included Eggerthella lentha, Ruminococcus, Bacteroides, with increase in abundance of Bacteroides stercoris. The early microbiome strongly predicts growth in the setting of modulator use for CwCF and we identify microbiome signatures associated with risk of being overweight. We highlight the possibility for interventions or early alternations to nutritional guidance for prevention of comorbid complications.

Evaluation of the microbiota-sparing properties of the anti-staphylococcal antibiotic afabicin.

Antibiotic use is associated with collateral damage to the healthy microbiota. Afabicin is a first-in-class prodrug inhibitor of the FabI enzyme that, when converted to the pharmacologically active agent afabicin desphosphono, demonstrates a staphylococcal-specific spectrum of activity. An expected benefit of highly targeted antibiotics such as afabicin is microbiome preservation. To compare the effects of oral treatment with afabicin and standard-of-care antibiotics upon the murine gut microbiota, and to assess the effects of oral afabicin treatment on the human gut microbiota. Gut microbiota effects of a 10 day oral course of afabicin treatment were monitored in mice and compared with clindamycin, linezolid and moxifloxacin at human-equivalent dose levels using 16S rDNA sequencing. Further, the gut microbiota of healthy volunteers was longitudinally assessed across 20 days of oral treatment with afabicin 240 mg twice daily. Afabicin treatment did not significantly alter gut microbiota diversity (Shannon H index) or richness (rarefied Chao1) in mice. Only limited changes to taxonomic abundances were observed in afabicin-treated animals. In contrast, clindamycin, linezolid and moxifloxacin each caused extensive dysbiosis in the murine model. In humans, afabicin treatment was not associated with alterations in Shannon H or rarefied Chao1 indices, nor relative taxonomic abundances, supporting the findings from the animal model. Oral treatment with afabicin is associated with preservation of the gut microbiota in mice and healthy subjects.

Skin and gut microbial associations with squamous cell carcinoma in solid organ transplant recipients.

Solid organ transplant recipients (SOTRs) are burdened with a significantly higher risk of squamous cell carcinoma (SCC) compared to the general population. Accumulating evidence suggests the potential influence of microbial dysbiosis on transplant outcomes. Based on these observations, we sought to identify differences in the cutaneous and gut microbiomes of SOTRs with and without a history of SCC. This case-control study collected and analyzed non-lesional skin and fecal samples of 20 SOTRs > 18years old with either ≥ 4 diagnoses of SCC since most recent transplant (n = 10) or 0 diagnoses of SCC (n = 10). The skin and gut microbiomes were investigated with Next-Generation Sequencing, and analysis of variance (ANOVA) followed by Tukey pairwise comparison procedure was used to test for differences in taxonomic relative abundances and microbial diversity indices between the two cohorts. Analyses of the skin microbiome showed increased bacterial and reduced fungal diversity in SOTRs with a history of SCC compared to SOTRs without a history of SCC (bacterial median Shannon diversity index (SDI) = 3.636 and 3.154, p < 0.05; fungal SDI = 4.474 and 6.174, p < 0.05, respectively). Analyses of the gut microbiome showed reduced bacterial and fungal diversity in the SCC history cohort compared to the SCC history-negative cohort (bacterial SDI = 2.620 and 3.300, p < 0.05; fungal SDI = 3.490 and 3.812, p < 0.05, respectively). The results of this pilot study thus show a trend toward the bacterial and fungal communities of the gut and skin being distinct in SOTRs with a history of SCC compared to SOTRs without a history of SCC. It furthermore demonstrates the potential for microbial markers to be used in the prognostication of squamous cell carcinoma risk in solid organ transplant recipients.

The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles

ABSTRACT The prevalence of anxiety and depression soared following the COVID-19 pandemic. To effectively treat these conditions, a comprehensive understanding of all etiological factors is needed. This study investigated fecal microbial features associated with mental health outcomes (symptoms of anxiety, depression, or posttraumatic stress disorder (PTSD)) in a Spanish cohort in the aftermath of the COVID-19 pandemic. Microbial communities from stool samples were profiled in 198 individuals who completed validated, self-report questionnaires. 16S ribosomal RNA gene V3-4 amplicon sequencing was performed. Microbial diversity and community structure were analyzed, together with relative taxonomic abundance. In our cohort of N=198, 17.17% reported depressive symptoms, 37.37% state anxiety symptoms, 40.90% trait anxiety symptoms, and 8.08% PTSD symptoms, with high levels of comorbidity. Individuals with trait anxiety had lower Simpson’s diversity. Fusicatenibacter saccharivorans was reduced in individuals with comorbid PTSD + depression + state and trait anxiety symptoms, whilst an expansion of Proteobacteria and depletion of Synergistetes phyla were noted in individuals with depressive symptoms. The relative abundance of Anaerostipes was positively correlated with childhood trauma, and higher levels of Turicibacter sanguinis and lower levels of Lentisphaerae were found in individuals who experienced life-threatening traumas. COVID-19 infection and vaccination influenced the overall microbial composition and were associated with distinct relative taxonomic abundance profiles. These findings will help lay the foundation for future studies to identify microbial role players in symptoms of anxiety, depression, and PTSD and provide future therapeutic targets to improve mental health outcomes.

Faunal exploitation during the Proto-Zhou period in the Jing River Valley: Evidence from Sunjia and Xitou

This study examines faunal assemblages from the Proto-Zhou sites of Sunjia and Xitou, in the Jing River Valley (Central Shaanxi Province), to address questions concerning the exploitation of different animal resources in the context of the Shang-Zhou dynastic transition in the 11th century BCE. Although the assemblages from Sunjia and Xitou were small and sub-optimally preserved, this study demonstrates that the inclusion of such assemblages is essential to building upon our understanding of the human exploitation of animal resources. Our zooarchaeological analysis shows an increase in husbandry, with pig farming being complemented by extensive caprine and cattle herding. A diversified use of animal resources, and especially the larger number of bovids, could have been prompted by the need for a wider and more efficient exploitation of the immediate environment, in response to growing climatic deterioration, in addition to an increase in interactions with northern pastoral communities. Identified patterns of livestock biometry and relative taxonomic abundance show various degrees of agricultural engagement and a relatively complex livestock economy, suggesting the development of socio-economic complexity in the Jing River Valley in the late second millennium BCE.

A network meta-analysis on comparison of invasive and non-invasive sampling methods to characterize intestinal microbiota of birds

Birds maintain complex and intimate associations with a diverse community of microbes in their intestine. Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses. However, the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings. Through performing a network meta-analysis for 13 published bird gut microbiome studies, here we attempt to investigate the comparability of these invasive and non-invasive sampling methods. The two most used non-invasive sampling methods (cloacal swabs and fecal samples) showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples. Overall, non-invasive samples showed decreased alpha diversity compared to intestinal samples, but the alpha diversities of fecal samples were more comparable to the intestinal samples. On the contrary, the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples, but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples. Phylogenetic status, diet, and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples. Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa, while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions. The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes.

The Effects of Iron Deficiency on the Gut Microbiota in Young Women

Background: Iron deficiency anemia (IDA) is highly prevalent worldwide, especially in premenopausal women during their reproductive years because of iron loss associated with menstruation and pregnancy. In 2019, the global prevalence of anemia was 36.5% among pregnant women, 29.6% in non-pregnant women Although iron is one of the most abundant elements on earth, it is not readily available for colonizing bacteria due to its low solubility in the human body. Hosts and microbiota compete fiercely for iron. Iron deficiency not only causes anemia, but also causes a variety symptoms including dyspnea, general weakness. Also, iron deficiency impact gut microbial health. There are some previous studies on the gut microbiome of patients with IDA. However, the study of the human microbiome is difficult to control for various variables that can influence the microbiome. To the best of our knowledge, there are limited studies regarding know the effects of iron supplementation on the gut microbiota in human. Aims: The aim of this study is to compare the microbiome of patients with IDA and normal individuals from young women. We also wanted to know the effects of iron supplementation on the gut microbiota. Methods: We enrolled 31 women in the study, including 15 IDA patients and 16 healthy volunteers. Participants, between 20 and 50 years of age, premenopausal women. All patients in the IDA group were diagnosed with IDA according to WHO diagnostic standards. Control participants were self-reported as healthy and did not suffer from an illness at the time of recruitment. Paticipants didn't use antibiotics and any other medical treatment that influences intestinal microbiota during 3 months before the study start. Stool sampling was conducted according to the Manual of Procedures for Human Microbiome Project Core Microbiome Sampling Protocol by the NIH at the time of study start. Following iron replacement for 3~6 months, the IDA patients performed a blood test to confirm that the anemia had improved, and stool sampling was conducted again at that time. Samples were obtained from 10 IDA patients before and after treatment with iron. 16S rRNA gene-based metagenomic analysis of fecal microbiome was performed. Results: Among the taxa with an average taxonomic composition greater than 1%, five classes (c-Coriobacteria, c-Negativicutes, c-Betaproteobacteria, c-Erysipelotrichi and c-Closteridia) and three orders (o-Clostridiales, o-Coriobacterials and o-Erysipelotrichales) significantly differ in three groups (Figure). Alpha diversity indices showed no differences between the groups and beta set-significance analysis indicated distinctive differences between normal and pre-treatment groups. Moreover, taxonomic biomarkers discovery by linear discriminant analysis Effect Size (LEfSe) analysis between normal and pre-treatment group showed higher effect size of f-Ruminococcaceae, o-Clostridiales, c-Clostridia, g-Faecalibacterium in normal and c-Negativicutes in pre-treatment group. Similarly, LEfSe analysis among treatment groups presented higher effect size of c-Erysipelotrichi, o-Erysipelotrichales, f-Erysipelotrichaceae in pre-treatment group. Whereas, LEfSe analysis between normal and post-treatment groups indicated that c-Coriobacteria, f-Coriobacteriaceae and o-Coriobacteriales were prominent in normal and g-Veillonella and g-Collinsella were significant in Post-treatment group. Finally, functional biomarker discovery by LEfSe analysis showed 15 Kos, 4 modules and two pathways distinctively different among the groups. Conclusions: In conclusion, there was a significant difference between the gut microbiome of the patients of IDA and that of healthy volunteers. We found a tendency of recovery of gut microbiome after iron supplementation treatment. Figure. Averaged taxonomic composition in stool of Normal, Pre- and Post-treatment IDA (iron deficiency anemia) groups. Taxonomic relative abundance was classified at the (A) phylum, (B) class, (C) order, (D) family, and (E) genus level, and relative abundances less than 1 % were expressed as ETC. Wilcoxon rank-sum test was used to analyze the significance between the two groups. a: Comparison between Normal and Pre; b: Comparison between Normal and Post; c: Comparison between Pre and Post;*, p<0.05. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Maternal anxiety, depression and stress affects offspring gut microbiome diversity and bifidobacterial abundances

Uncovering mechanisms underlying fetal programming during pregnancy is of critical importance. Atypical neurodevelopment during the pre- and immediate postnatal period has been associated with long-term adverse health outcomes, including mood disorders and aberrant cognitive ability in offspring. Maternal factors that have been implicated in anomalous offspring development include maternal inflammation and tress, anxiety, and depression.One potential mechanism through which these factors perturb normal offspring postnatal development is through microbiome disruption. The mother is a primary source of early postnatal microbiome seeding for the offspring, and the transference of a healthy microbiome is key in normal neurodevelopment. Since psychological stress, mood disorders, and inflammation have all been implicated in altering maternal microbiome community structure, passing on aberrant microbial communities to the offspring that may then affect developmental outcomes. Therefore, we examined how maternal stress, anxiety and depression assessed with standardized instruments, and maternal inflammatory cytokine levels in the pre- and postnatal period are associated with the offspring microbiome within the first 13 months of life, utilizing full length 16S sequencing on infant stool samples, that allowed for species-level resolution.Results revealed that infants of mothers who reported higher anxiety and perceived stress had reduced alpha diversity. Additionally, the relative taxonomic quantitative abundances of Bifidobacterium dentium and other species that have been associated with either modulation of the gut-brain axis, or other beneficial health outcomes, were reduced in the offspring of mothers with higher anxiety, perceived stress, and depression. We also found associations between bifidobacteria and prenatal maternal pro-inflammatory cytokines IL-6, IL-8, and IL-10. In summary, specific microbial taxa involved in maintaining proper brain and immune function are lower in offspring born to mothers with anxiety, depression, or stress, providing strong evidence for a mechanism by which maternal factors may affect offspring health through microbiota dysregulation.

Host-specific epibiomes of distinct Acropora cervicornis genotypes persist after field transplantation

Microbiome studies across taxa have established the influence of host genotype on microbial recruitment and maintenance. However, research exploring host-specific epibionts in scleractinian corals is scant, and the influence of intraspecific differences across environments remains unclear. Here, we studied ten Acropora cervicornis genotypes to investigate the relative roles of host genotype and environment in structuring the epibiome. Coral mucus was sampled in a common garden nursery from replicate ramets of distinct genotypes (T0). Coral fragment replicates (n = 3) of each genotype were then transplanted to nine different field sites in the Lower Florida Keys, and mucus was again sampled one year later from surviving ramets (T12). 16S rRNA amplicon sequencing was used to assess microbial composition, richness, and beta-diversity. The most abundant and consistent amplicon sequencing variants (ASVs) in all samples belonged to Midichloriaceae (MD3-55 genus) and Cyanobacteria (Synechococccus). The relative abundances of these bacterial taxa varied consistently between genotypes, whereas neither the composition nor taxonomic relative abundance were significantly different among field sites. Interestingly, several high MD3-55 hosting genotypes showed rapid diversification and an increase in MD3-55 following transplantation. Overall, our results indicate healthy A. cervicornis genotypes retain distinct epibiome signatures through time, suggesting a strong host component. Lastly, our results show that differences in MD3-55 abundances can be consistently detected in the epibiome of distinct host genotypes of A. cervicornis. As this organism (sensu Aquarickettsia rohweri) has been implicated as a marker of disease resistance, this finding reinforces the potential use of microbial indicators in reef restoration efforts via non-invasive surface/mucus sampling.

1064. Treatment Success in Reducing Recurrent Clostridioides difficile Infection with Investigational Live Biotherapeutic RBX2660 Is Associated with Microbiota Restoration: Consistent Evidence from a Phase 3 Clinical Trial

BackgroundSeveral investigational microbiota-based live biotherapeutics are in clinical development for reducing recurrence of Clostridioides difficile infection (rCDI), including RBX2660 a liquid suspension of a broad consortium of microbiota, which includes Bacteridetes and Firmicutes. RBX2660 has been evaluated in >600 participants in 6 clinical trials. Here we report that RBX2660 induced significant shifts to the intestinal microbiota of treatment-responsive participants in PUNCH CD3—a Phase 3 randomized, double-blinded, placebo-controlled trial.MethodsPUNCH CD3 participants received a single dose of RBX2660 or placebo between 24 to 72 hours after completing rCDI antibiotic treatment. Clinical response was the absence of CDI recurrence at eight weeks after treatment. Participants voluntarily submitted stool samples prior to blinded study treatment (baseline), 1, 4 and 8 weeks, 3 and 6 months after receiving study treatment. Samples were extracted and sequenced using shallow shotgun methods. Operational taxonomic unit (OTU) data were used to calculate relative taxonomic abundance, alpha diversity, and the Microbiome Health Index (MHI)—a biomarker of antibiotic-induced dysbiosis and restoration.ResultsClinically, RBX2660 demonstrated superior efficacy versus placebo (70.4% versus 58.1%). From before to after treatment, RBX2660-treated clinical responders’ microbiome diversity shifted significantly (Mann-Whitney), and so did microbiome composition (Generalized Wald Test). Post-treatment changes were characterized by increased Bacteroidia and Clostridia and decreased Gammaproteobacteria and Bacilli, changes and were durable to at least 6 months. Repeated measures analysis confirmed that shifts were greater among RBX2660 responders compared to placebo responders (DMRepeat). The majority of responders’ MHI values shifted from a range common to antibiotic dysbiosis to a range common in healthy populations.Figure 1 Left panel. Mean relative abundance taxonomic class level at timepoints for participants in PUNCH CD3 before and after RBX2660 treatment, and for doses of RBX2660 administered in PUNCH CD3. The four taxonomic classes that change most from before to after treatment are shown with the mean and confidence intervals based on fitting OTU data to a Dirichlet multinomial distribution. Right panel, MHI biomarker for the same time points and investigational product groups, shown as median (red) and individual samples. A previously calculated threshold of MHI = 7.2 is shown (dotted line), above which MHI values predict healthy, below which MHI values predict antibiotic-induced dysbiosis.ConclusionAmong PUNCH CD3 clinical responders, RBX2660 significantly restored microbiota from less to more healthy compositions, and this restoration was durable to at least 6 months. These clinically-correlated microbiome shifts are highly consistent with results from multiple prior trials of RBX2660.Disclosures Ken Blount, PhD, Rebiotix Inc., a Ferring Company (Employee) Dana M. Walsh, PhD, Rebiotix (Employee)

191P Fecal microbiome in soft-tissue sarcoma (STS) patients treated with neoadjuvant immune checkpoint blockade (ICB)

191P Fecal microbiome in soft-tissue sarcoma (STS) patients treated with neoadjuvant immune checkpoint blockade (ICB)

Alterations of lung microbial communities in obese allergic asthma and metabolic potential.

In recent years, there has been a rapid increase in microbiome studies to explore microbial alterations causing disease status and unveil disease pathogenesis derived from microbiome environmental modifications. Convincing evidence of lung microbial changes involving asthma has been collected; however, whether lung microbial changes under obesity leads to severe asthma in a state of allergen exposure has not been studied sufficiently. Here, we measured bacterial alterations in the lung of an allergen mouse model induced by a high fat diet (HFD) by using 16S rRNA gene sequencing. A total of 33 pathogen‑free 3‑week‑old male C57BL/6 mice were used, and they divided randomly into two groups. The Chow diet (n = 16) and high fat diet (n = 17) was administrated for 70 days. Mice were sensitized with PBS or Dermatophagoides pteronyssinus extract (Der.p), and concentration levels of total IgE and Der.p-IgE in the blood were measured to quantify immune responses. Although there were no meaningful differences in bacterial species richness in the HFD mouse group, momentous changes of bacterial diversity in the HFD mouse group were identified after the mouse group was exposed to allergens. At a genus level, the fluctuations of taxonomic relative abundances in several bacteria such as Ralstonia, Lactobacillus, Bradyrhizobium, Gaiella, PAC001932_g, Pseudolabrys, and Staphylococcus were conspicuously observed in the HFD mouse group exposed to allergens. Also, we predicted metabolic signatures occurring under microbial alterations in the Chow group versus the Chow group exposed to allergens, as well as in the HFD mouse group versus the HFD group exposed to allergens. We then compared their similarities and differences. Metabolic functions associated with macrophages such as propanoate metabolism, butanoate metabolism, and glycine-serine-threonine metabolism were identified in the HFD group versus the Chow group. These results provide new insights into the understanding of a microbiome community of obese allergic asthma, and shed light on the functional roles of lung microbiota inducing the pathogenesis of severe asthma.

Selective butanol production from carbon monoxide by an enriched anaerobic culture

An anaerobic mixed culture able to grow on pure carbon monoxide (CO) as well as syngas (CO, CO2 and H2), that produced unusual high concentrations of butanol, was enriched in a bioreactor with intermittent CO gas feeding. At pH 6.2, it mainly produced acids, generally acetic and butyric acid. After adaptation, under stress conditions of CO exposure at a partial pressure of 1.8 bar and low pH (e.g., 5.7), the enrichment accumulated ethanol, but also high amounts of butanol, up to 6.8 g/L, never reported before, with a high butanol/butyric acid molar ratio of 12.6, highlighting the high level of acid to alcohol conversion. At the end of the assay, both the acetic acid and ethanol concentrations decreased, with concomitant butyric acid production, suggesting C2 to C4 acid bioconversion, though this was not a dominant bioconversion process. The reverse reaction of ethanol oxidation to acetic acid was observed in the presence of CO2 produced during CO fermentation. Interestingly, butanol oxidation with simultaneous butyric acid production occurred upon production of CO2 from CO, which has to the best of our knowledge never been reported. Although the sludge inoculum contained a few known solventogenic Clostridia, the relative taxonomic abundance of the enriched sludge was diverse in Clostridia and Bacilli classes, containing known solventogens, e.g., Clostridium ljungdhalii, Clostridium ragsdalei and Clostridium coskatii, confirming their efficient enrichment. The relative abundance of unassigned Clostridium species amounted to 27% with presumably novel ethanol/butanol producers.

Associations between the gut microbiome and metabolome in early life

BackgroundThe infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationship within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life.ResultsStool samples collected from infants enrolled in the New Hampshire Birth Cohort Study (NHBCS) at approximately 6-weeks (n = 158) and 12-months (n = 282) of age were profiled using targeted and untargeted nuclear magnetic resonance (NMR) spectroscopy as well as DNA sequencing of the V4-V5 hypervariable region from the bacterial 16S rRNA gene. There was significant inter-omic concordance based on Procrustes analysis (6 weeks: p = 0.056; 12 months: p = 0.001), however this association was no longer significant when accounting for phylogenetic relationships using generalized UniFrac distance metric (6 weeks: p = 0.376; 12 months: p = 0.069). Sparse canonical correlation analysis showed significant correlation, as well as identifying sets of microbe/metabolites driving microbiome-metabolome relatedness. Performance of machine learning models varied across different metabolites, with support vector machines (radial basis function kernel) being the consistently top ranked model. However, predictive R2 values demonstrated poor predictive performance across all models assessed (avg: − 5.06% -- 6 weeks; − 3.7% -- 12 months). Conversely, the Spearman correlation metric was higher (avg: 0.344–6 weeks; 0.265–12 months). This demonstrated that taxonomic relative abundance was not predictive of metabolite concentrations.ConclusionsOur results suggest a degree of overall association between taxonomic profiles and metabolite concentrations. However, lack of predictive capacity for stool metabolic signatures reflects, in part, the possible role of functional redundancy in defining the taxa-function relationship in early life as well as the bidirectional nature of the microbiome-metabolome association. Our results provide evidence in favor of a multi-omic approach for microbiome studies, especially those focused on health outcomes.

Herpetofaunal diversity changes with climate: evidence from the Quaternary of McEachern’s Deathtrap Cave, southeastern Australia

ABSTRACT The Quaternary Period is characterized by dramatic global climatic changes. Quaternary fossil deposits, which can offer excellent stratigraphic resolution, provide a unique opportunity to understand how fauna respond to past environmental change. Here, we test if the herpetofauna of McEachern’s Deathtrap Cave, a late Pleistocene to Holocene pitfall trap deposit from Victoria, Australia, shows climate-related shifts in taxonomic relative abundance through time. During the last 14,000 years, southeastern Australia experienced pronounced periods of aridity, while temperatures remained relatively stable. We show that the stratigraphic layers of this deposit are characterized by different relative abundances of reptile subfamilies, and that changes in subfamily abundance between layers correlate with known shifts to aridity, based on the percentage of C4 grasses present in the region. We further identify 13 lizard morphotypes from the fossil deposit and compare this diversity with the present-day lizard fauna. Our analyses indicate that gradual changes in community structure, which are typically observed in southeastern Australian vertebrate communities during the Pleistocene–Holocene transition, can partly be explained by changing aridity. These findings represent an important contribution to understanding Quaternary community change in Australia, particularly because evidence of faunal succession of reptile and amphibian communities in Victoria is lacking. Our results further demonstrate the utility of the Australian herpetofaunal fossil record for detecting community responses to past climate change on relatively shallow timescales and at higher levels of taxonomic identification.

Comparison of 16S and whole genome dog microbiomes using machine learning

BackgroundRecent advances in sequencing technologies have driven studies identifying the microbiome as a key regulator of overall health and disease in the host. Both 16S amplicon and whole genome shotgun sequencing technologies are currently being used to investigate this relationship, however, the choice of sequencing technology often depends on the nature and experimental design of the study. In principle, the outputs rendered by analysis pipelines are heavily influenced by the data used as input; it is then important to consider that the genomic features produced by different sequencing technologies may emphasize different results.ResultsIn this work, we use public 16S amplicon and whole genome shotgun sequencing (WGS) data from the same dogs to investigate the relationship between sequencing technology and the captured gut metagenomic landscape in dogs. In our analyses, we compare the taxonomic resolution at the species and phyla levels and benchmark 12 classification algorithms in their ability to accurately identify host phenotype using only taxonomic relative abundance information from 16S and WGS datasets with identical study designs. Our best performing model, a random forest trained by the WGS dataset, identified a species (Bacteroides coprocola) that predominantly contributes to the abundance of leuB, a gene involved in branched chain amino acid biosynthesis; a risk factor for glucose intolerance, insulin resistance, and type 2 diabetes. This trend was not conserved when we trained the model using 16S sequencing profiles from the same dogs.ConclusionsOur results indicate that WGS sequencing of dog microbiomes detects a greater taxonomic diversity than 16S sequencing of the same dogs at the species level and with respect to four gut-enriched phyla levels. This difference in detection does not significantly impact the performance metrics of machine learning algorithms after down-sampling. Although the important features extracted from our best performing model are not conserved between the two technologies, the important features extracted from either instance indicate the utility of machine learning algorithms in identifying biologically meaningful relationships between the host and microbiome community members. In conclusion, this work provides the first systematic machine learning comparison of dog 16S and WGS microbiomes derived from identical study designs.

Taxonomic changes in the gut microbiota are associated with cartilage damage independent of adiposity, high fat diet, and joint injury

Lipodystrophic mice are protected from cartilage damage following joint injury. This protection can be reversed by the implantation of a small adipose tissue graft. The purpose of this study was to evaluate the relationship between the gut microbiota and knee cartilage damage while controlling for adiposity, high fat diet, and joint injury using lipodystrophic (LD) mice. LD and littermate control (WT) mice were fed a high fat diet, chow diet, or were rescued with fat implantation, then challenged with destabilization of the medial meniscus surgery to induce osteoarthritis (OA). 16S rRNA sequencing was conducted on feces. MaAslin2 was used to determine associations between taxonomic relative abundance and OA severity. While serum LPS levels between groups were similar, synovial fluid LPS levels were increased in both limbs of HFD WT mice compared to all groups, except for fat transplanted animals. The Bacteroidetes:Firmicutes ratio of the gut microbiota was significantly reduced in HFD and OA-rescued animals when compared to chow. Nine novel significant associations were found between gut microbiota taxa and OA severity. These findings suggest the presence of causal relationships the gut microbiome and cartilage health, independent of diet or adiposity, providing potential therapeutic targets through manipulation of the microbiome.

Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Pilot Study.

We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6–8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.

Dietary Variety Relates to Gut Microbiota Diversity and Abundance

ObjectivesCumulative evidence indicated dietary intake is associated with gut microbiota. This study aim to investigate the association between Dietary Variety Score (DVS) and the Index of Nutritional Quality (INQ) and gut microbiota in healthy individuals. MethodsIn this cross-sectional study, we analyzed gut microbiota composition and structure using 16S rRNA gene (V4-V5 region) sequencing of 128 participants. Dietary frequency and 24-h dietary consumption was ascertained using an FFQ. Differences in α- and β-diversity and taxonomic relative abundances between the higher and lower DVS and INQs were compared, followed by multivariable analyses. ResultsThe structure of the microbiota significantly differed by dietary variety. A lower score for DVS was associated with significantly lower richness (Shannon index P = 0.0096). The INQ of vitamin E (INQVE), Zinc (INQZn) and vitamin B6 (INQB6) correlated positively with the Shannon index (rho = 0.235, P = 0.008 for INQVE; rho = 0.209, P = 0.019 for INQZn; rho = 0.182, P = 0.040 for INQB6). A cumulative higher score of INQZn, INQB6 and INQVE was associated with significantly higher richness (Shannon index p-trend = 0.001). A lower score for DVS was associated with significantly reduced relative abundance of genus on Alistipes, Megasphaera and Barnesiella but higher Roseburia and Haemophilus. A lower score for INQVE was associated with significantly reduced relative abundance of genus on Coprococcus and Romboutsia. A lower score for INQB6 was associated with significantly reduced relative abundance of genus on Lachnospira, Dorea, Butyricicoccus, and Anaerostipes but higher Lachnoclostridium (the linear discriminant analysis effect size (LEfSe) >3). Meanwhile, the abundance of Coprococcus significantly increased with the higher cumulative score of INQVE, INQZn and INQB6 (P < 0.01), and it associated negatively with LDL level (coef = –0.264, P = 0.041). The findings were confirmed by multivariate analysis. ConclusionsLower dietary variety was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the healthy individuals. Funding SourcesThis work was supported by the National Natural Science Foundation of China (No.82,060,593), Natural Science Foundation of Guangxi Province (No. 2018GXNSFDA050019).