Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome.

While conventional pathogenic protists have been extensively studied, there is an underappreciated constitutive protist microbiota that is an integral part of the vertebrate microbiome. The impact of these species on the host and their potential contributions to mucosal immune homeostasis remain poorly studied. Here, we show that the protozoan Tritrichomonas musculis activates the host epithelial inflammasome to induce IL-18 release. Epithelial-derived IL-18 promotes dendritic cell-driven Th1 and Th17 immunity and confers dramatic protection from mucosal bacterial infections. Along with its role as a "protistic" antibiotic, colonization with T. musculis exacerbates the development of T-cell-driven colitis and sporadic colorectal tumors. Our findings demonstrate a novel mutualistic host-protozoan interaction that increases mucosal host defenses at the cost of an increased risk of inflammatory disease.

Advancing the microbiome research community.

The human microbiome has become a recognized factor in promoting and maintaining health. We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. Advances in these aspects of the research community may in turn advance our understanding of human microbiome biology.

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.

Microbiota are thought to influence the development and progression of inflammatory bowel disease (IBD), but determining generalizable effects of microbiota on IBD etiology requires larger-scale functional analyses. We colonized germ-free mice with intestinal microbiotas from 30 healthy and IBD donors and determined the homeostatic intestinal T cell response to each microbiota. Compared to microbiotas from healthy donors, transfer of IBD microbiotas into germ-free mice increased numbers of intestinal Th17 cells and Th2 cells and decreased numbers of RORγt+ Treg cells. Colonization with IBD microbiotas exacerbated disease in a model where colitis is induced upon transfer of naive T cells into Rag1-/- mice. The proportions of Th17 and RORγt+ Treg cells induced by each microbiota were predictive of human disease status and accounted for disease severity in the Rag1-/- colitis model. Thus, an impact on intestinal Th17 and RORγt+ Treg cell compartments emerges as a unifying feature of IBD microbiotas, suggesting a general mechanism for microbial contribution to IBD pathogenesis.

The impact of the gut microbiota on human health: an integrative view.

The human gut harbors diverse microbes that play a fundamental role in the well-being of their host. The constituents of the microbiota--bacteria, viruses, and eukaryotes--have been shown to interact with one another and with the host immune system in ways that influence the development of disease. We review these interactions and suggest that a holistic approach to studying the microbiota that goes beyond characterization of community composition and encompasses dynamic interactions between all components of the microbiota and host tissue over time will be crucial for building predictive models for diagnosis and treatment of diseases linked to imbalances in our microbiota.

Identifying correlations driven by influential observations in large datasets.

Although high-throughput data allow researchers to interrogate thousands of variables simultaneously, it can also introduce a significant number of spurious results. Here we demonstrate that correlation analysis of large datasets can yield numerous false positives due to the presence of outliers that canonical methods fail to identify. We present Correlations Under The InfluencE (CUTIE), an open-source jackknifing-based method to detect such cases with both parametric and non-parametric correlation measures, and which can also uniquely rescue correlations not originally deemed significant or with incorrect sign. Our approach can additionally be used to identify variables or samples that induce these false correlations in high proportion. A meta-analysis of various omics datasets using CUTIE reveals that this issue is pervasive across different domains, although microbiome data are particularly susceptible to it. Although the significance of a correlation eventually depends on the thresholds used, our approach provides an efficient way to automatically identify those that warrant closer examination in very large datasets.

Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate Chronic Obstructive Pulmonary Disease.

Rationale: Chronic obstructive pulmonary disease (COPD) is associated with high morbidity, mortality, and healthcare costs. Cigarette smoke is a causative factor; however, not all heavy smokers develop COPD. Microbial colonization and infections are contributing factors to disease progression in advanced stages. Objectives: We investigated whether lower airway dysbiosis occurs in mild-to-moderate COPD and analyzed possible mechanistic contributions to COPD pathogenesis. Methods: We recruited 57 patients with a >10 pack-year smoking history: 26 had physiological evidence of COPD, and 31 had normal lung function (smoker control subjects). Bronchoscopy sampled the upper airways, lower airways, and environmental background. Samples were analyzed by 16S rRNA gene sequencing, whole genome, RNA metatranscriptome, and host RNA transcriptome. A preclinical mouse model was used to evaluate the contributions of cigarette smoke and dysbiosis on lower airway inflammatory injury. Measurements and Main Results: Compared with smoker control subjects, microbiome analyses showed that the lower airways of subjects with COPD were enriched with common oral commensals. The lower airway host transcriptomics demonstrated differences in markers of inflammation and tumorigenesis, such as upregulation of IL-17, IL-6, ERK/MAPK, PI3K, MUC1, and MUC4 in mild-to-moderate COPD. Finally, in a preclinical murine model exposed to cigarette smoke, lower airway dysbiosis with common oral commensals augments the inflammatory injury, revealing transcriptomic signatures similar to those observed in human subjects with COPD. Conclusions: Lower airway dysbiosis in the setting of smoke exposure contributes to inflammatory injury early in COPD. Targeting the lower airway microbiome in combination with smoking cessation may be of potential therapeutic relevance.

Relative Match Load in Young Professional Soccer Players during Soccer-7 and Soccer-11.

The aim of this study was to analyze the differences in internal and external load during Soccer-7 and Soccer-11, comparing positional requirements and neuromuscular fatigue in both modalities. Twenty-four young soccer players were monitored in Soccer-7 and Soccer-11 matches using global positioning systems. Total distance covered (TD), distance covered at high speed (HSR), distance covered at very high speed (VHSR), peak speed, accelerations (Acc) and decelerations (Dec) and rate of perceived exertion (RPE) were recorded differentiating between central backs (CB), midfielders (MF), external players (EX) and forwards (FW). Neuromuscular fatigue were assessed using a jump test. During Soccer-11, players showed significantly higher TD, HSR and VHSR, with low Acc and greater RPE compared with Soccer-7. During Soccer-11, all positions recorded significantly greater TD, distance at HSR and at VHSR than Soccer-7. In terms of playing position, CB, MF and FW achieved significantly higher Peak Speed during Soccer-1, but there was no difference for EX. During Soccer-7 all positions performed significantly higher numbers of Acc. Although the Soccer-7 modality is considered an optimal format for the development of young soccer players, there is a significant difference in match running activity for all playing positions with respect to the Soccer-11 format.

Influence of the Number of Players on the Load of Soccer Players During Transition Games.

The aims of this study were to determine the effect of different compositions in transition games (TGs) on the load of soccer players and to evaluate their performance in physical tests. Using a GPS system, 18 players were monitored during: 3vs2, 2vs1 and 1vs1. Distance covered (DC), DC 18-20.9 km·h-1, 21-23.9 km·h-1,>24 km·h-1, peak speed, accelerations (Acc) and decelerations (Dec)>1.0 m·s-2 and>2.5 m·s-2 and rate of perceived exertion (RPE) were recorded. Before and after each TG, countermovement-jump (CMJ), 15- (S15) and 30 m (S30) speed tests were assessed. TG3vs2 showed greater DC and Dec>1.0 m·s-2 than TG2vs1, and DC, DC 18.0-23.9 km·h-1, Acc>1.0 m·s-2 and Dec>2.5 m·s-2 than TG1vs1 (p<0.01). TG2vs1 achieved higher DC, DC 18.0-23.9 km·h-1, and Acc>2.5 m·s-2 (p<0.01) but lower peak speed (p=0.02) and RPE (p=0.02) than TG1vs1. Post-intervention, TG1vs1 showed lower CMJ and higher S15 (p=0.02), while TG3vs2, showed improvements in CMJ (p<0.01). The three tasks showed large variations for DC>24 km·h-1, Acc>1.0 m·s-2, Dec>1.0 m·s-2 and Dec>2.5 m·s-2. The load of TGs is sensitive to their player composition.

More than Mycobacterium tuberculosis: site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis.

BACKGROUND: Lymphadenitis is the most common extrapulmonary tuberculosis (EPTB) manifestation. The microbiome is important to human health but uninvestigated in EPTB. We profiled the site-of-disease lymph node microbiome in tuberculosis lymphadenitis (TBL). METHODS: Fine-needle aspiration biopsies were collected from 158 pretreatment presumptive TBL patients in Cape Town, South Africa. 16S Illumina MiSeq rRNA gene sequencing was done. RESULTS: We analysed 89 definite TBLs (dTBLs) and 61 non-TBLs (nTBLs), which had similar α- but different ß-diversities (p=0.001). Clustering identified five lymphotypes prior to TB status stratification: Mycobacterium-dominant, Prevotella-dominant and Streptococcus-dominant lymphotypes were more frequent in dTBLs whereas a Corynebacterium-dominant lymphotype and a fifth lymphotype (no dominant taxon) were more frequent in nTBLs. When restricted to dTBLs, clustering identified a Mycobacterium-dominant lymphotype with low α-diversity and non-Mycobacterium-dominated lymphotypes (termed Prevotella-Corynebacterium, Prevotella-Streptococcus). The Mycobacterium dTBL lymphotype was associated with HIV-positivity and features characteristic of severe lymphadenitis (eg, larger nodes). dTBL microbial communities were enriched with potentially proinflammatory microbial short-chain fatty acid metabolic pathways (propanoate, butanoate) vs nTBLs. 11% (7/61) of nTBLs had Mycobacterium reads BLAST-confirmed as Mycobacterium tuberculosis complex. CONCLUSIONS: TBL at the site-of-disease is not microbially homogeneous. Distinct microbial community clusters exist that, in our setting, are associated with different clinical characteristics, and immunomodulatory potentials. Non-Mycobacterium-dominated dTBL lymphotypes, which contain taxa potentially targeted by TB treatment, were associated with milder, potentially earlier stage disease. These investigations lay foundations for studying the microbiome's role in lymphatic TB. The long-term clinical significance of these lymphotypes requires prospective validation.

Alterations in the cutaneous microbiome of patients with psoriasis and psoriatic arthritis reveal similarities between non-lesional and lesional skin.

OBJECTIVES: To investigate the cutaneous microbiome spanning the entire psoriatic disease spectrum, and to evaluate distinguishing features of psoriasis (PsO) and psoriatic arthritis (PsA). METHODS: Skin swabs were collected from upper and lower extremities of healthy individuals and patients with PsO and PsA. Psoriatic patients contributed both lesional (L) and contralateral non-lesional (NL) samples. Microbiota were analysed using 16S rRNA sequencing. RESULTS: Compared with healthy skin, alpha diversity in psoriatic NL and L skin was significantly reduced (p<0.05) and samples clustered separately in plots of beta diversity (p<0.05). Kocuria and Cutibacterium were enriched in healthy subjects, while Staphylococcus was enriched in psoriatic disease. Microbe-microbe association networks revealed a higher degree of similarity between psoriatic NL and L skin compared with healthy skin despite the absence of clinically evident inflammation. Moreover, the relative abundance of Corynebacterium was higher in NL PsA samples compared with NL PsO samples (p<0.05), potentially serving as a biomarker for disease progression. CONCLUSIONS: These findings show differences in diversity, bacterial composition and microbe-microbe interactions between healthy and psoriatic skin, both L and NL. We further identified bacterial biomarkers that differentiate disease phenotypes, which could potentially aid in predicting the transition from PsO to PsA.

Coherence and divergence in autonomic-subjective affective space.

A central tenet of many theories of emotion is that emotional states are accompanied by distinct patterns of autonomic activity. However, experimental studies of coherence between subjective and autonomic responses during emotional states provide little evidence of coherence. Crucially, previous studies investigating coherence have either adopted univariate approaches or made limited use of multivariate analytic approaches by investigating subjective and autonomic responses separately. The current study addressed this question using a multivariate dimensional approach to build a common autonomic-subjective affective space incorporating subjective responses and three different autonomic signals (heart rate, skin conductance response, and pupil diameter), measured during an emotion-inducing task, in 51 participants. Results showed that autonomic and subjective responses could be adequately described in a two-dimensional affective space. The first dimension included contributions from subjective and autonomic responses, indicating coherence, while contributions to the second dimension were almost exclusively of autonomic covariance. Thus, while there was a degree of coherence between autonomic and subjective emotional responses, there was substantial structure in autonomic responses that did not covary with subjective emotional experience. This study, therefore, contributes new insights into the relationship between subjective and autonomic emotional responses, and provides a framework for future multimodal emotion research, enabling both hypothesis- and data-driven testing.

Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas.

The building evidence for the contribution of microbiota to human disease has spurred an effort to develop therapies that target the gut microbiota. This is particularly evident in inflammatory bowel diseases (IBDs), where clinical trials of fecal microbiota transplantation have shown some efficacy. To aid the development of novel microbiota-targeted therapies and to better understand the biology underpinning such treatments, we have used gnotobiotic mice to model microbiota manipulations in the context of microbiotas from humans with inflammatory bowel disease. Mice colonized with IBD donor-derived microbiotas exhibit a stereotypical set of phenotypes, characterized by abundant mucosal Th17 cells, a deficit in the tolerogenic RORγt+ regulatory T (Treg) cell subset, and susceptibility to disease in colitis models. Transplanting healthy donor-derived microbiotas into mice colonized with human IBD microbiotas led to induction of RORγt+ Treg cells, which was associated with an increase in the density of the microbiotas following transplant. Microbiota transplant reduced gut Th17 cells in mice colonized with a microbiota from a donor with Crohn's disease. By culturing strains from this microbiota and screening them in vivo, we identified a specific strain that potently induces Th17 cells. Microbiota transplants reduced the relative abundance of this strain in the gut microbiota, which was correlated with a reduction in Th17 cells and protection from colitis.

Effects of Bout Duration on Load, Sprint, and Jump Ability During a One-on-one Transition Task.

This study examined the training load on professional soccer players during transition games performed with different bout durations and their effects on speed and jump tests. Fourteen young soccer players played a transition game of different bout durations: 15 (TG15), 30 (TG30), and 60 (TG60) seconds. Total distance covered (DC), accelerations and decelerations above 1.0 and 2.5 m·s-2, rate of perceived exertion (RPE), maximal heart rate (HRmax) and above 90% (HR>90), distance covered between 18.0-20.9 km·h-1 (DC 18.0-20.9 km·h-1), 21.0-23.9 km·h-1 (DC 21.0-23.9 km·h-1), above 24.0 km·h-1 (DC>24.0 km·h-1), peak speed, sprint profile, sprint, and countermovement jump tests were recorded. TG15 obtained greater DC, DC>21.0 km·h-1, Player load, Acc>2.5 m·s-2 than TG30 and TG60 (p<0.01) and Acc<2.5 m·s-2, Dec>2.5 m·s-2 than TG60 (p<0.01). TG30 showed more HR>90 and RPE (p<0.01) than TG15, and DC, DC>18.0 km·h-1, Player load, Acc>2.5 m·s-2, Dec>2.5 m·s-2, HR>90 and RPE than TG60 (p<0.01 and<0.05). Transition games showed lower sprint and jump results after the intervention (p<0.01). Bout duration has been configured as an important constraint that influences the transition games and the performance of soccer players.

Different pitch configurations constrain the external and internal loads of young professional soccer players during transition games.

The aims of this study were to compare the influence of transition game (TG) size on the external and internal loads of young professional soccer players and to describe the high-speed profile of these drills in response to pitch dimensions. Eighteen young professional soccer players (age: 16.1 ± 0.3 years; height: 178.3 ± 5.4 cm; weight: 70.1 ± 6.2 kg) performed a 3vs2 TG on pitches measuring 40 × 30 m (TG30), 40 × 50 m (TG50) and 40 × 70 m (TG70) m. Distance covered (DC); accelerations-decelerations above 1.0 m · s-2 and 2.5 m · s-2; rate of perceived exertion (RPE); maximal heart rate and time above 90%; DC at 18.0 to 21.0 km · h-1 (DC 18-20.9 km · h-1); DC at 21.0 to 23.9 km · h-1 (DC 21-23.9 km · h-1); DC above 24.0 km · h-1 (DC > 24 km · h-1); and peak speed and sprint profile (duration, distance and maximal speed) were measured. TG30 achieved lower DC, DC above 18 km · h-1, peak speed, sprint distance and RPE than TG50 and TG70 (p < 0.01 and p < 0.05) and lower sprint duration and maximal speed sprint than TG70 (p < 0.01). TG30 and TG50 achieved higher Acc > 1.0 and > 2.5 m · s-2 respectively than TG70 (p < 0.05). TG70 showed greater DC above 21 km · h-1, peak speed, sprint distance and maximal speed sprint than TG50 (p < 0.01). Soccer coaches should use larger TGs to overload variables related to high speed and sprint demands during training and smaller TG formats to stimulate the accelerations of the soccer players.

Impaired central tolerance induces changes in the gut microbiota that exacerbate autoimmune hepatitis.

Medullary thymic epithelial cells (mTECs) induce T cell tolerance in the thymus through the elimination of self-reactive thymocytes. Commensal bacteria are also critical for shaping T cell responses in the gut and distal organs. We previously showed that mice depleted of mTECs (Traf6ΔTEC) generated autoreactive T cells and developed autoimmune hepatitis (AIH). In this report, we found that Toll-like receptor (TLR)-mediated microbial sensing on liver hematopoietic cells and the gut microbiota contributed to AIH development in Traf6ΔTEC mice. While adoptive transfer of thymic Traf6ΔTEC T cells in immune-deficient mice was sufficient for AIH development, colonization of germ-free mice with Traf6ΔTEC microbiota failed to induce AIH, suggesting that the gut microbiota contributes to but is not sufficient for AIH development. Microbiota-mediated exacerbation of AIH associated with increased numbers of hepatic Foxp3+ T cells and their increase was proportional to the degree of inflammation. The contribution of the gut microbiota to AIH development associated with an altered microbial signature whose composition was influenced by the qualitative nature of the thymic T cell compartment. These results suggest that aberrant selection of T cells in the thymus can induce changes in the gut microbiota that lead to exacerbation of organ-specific autoimmunity and AIH. Our results add to our understanding of the mechanisms of AIH development and create a platform towards developing novel therapeutic approaches for treating this disease.

Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary T-Helper Cell Type 17 Response that Mitigates Susceptibility to Streptococcus pneumoniae.

Rationale: Cross-sectional human data suggest that enrichment of oral anaerobic bacteria in the lung is associated with an increased T-helper cell type 17 (Th17) inflammatory phenotype.Objectives: In this study, we evaluated the microbial and host immune-response dynamics after aspiration with oral commensals using a preclinical mouse model.Methods: Aspiration with a mixture of human oral commensals (MOC; Prevotella melaninogenica, Veillonella parvula, and Streptococcus mitis) was modeled in mice followed by variable time of killing. The genetic backgrounds of mice included wild-type, MyD88-knockout, and STAT3C backgrounds.Measurements and Main Results: 16S-rRNA gene sequencing characterized changes in microbiota. Flow cytometry, cytokine measurement via Luminex and RNA host-transcriptome sequencing was used to characterize the host immune phenotype. Although MOC aspiration correlated with lower-airway dysbiosis that resolved within 5 days, it induced an extended inflammatory response associated with IL-17-producing T cells lasting at least 14 days. MyD88 expression was required for the IL-17 response to MOC aspiration, but not for T-cell activation or IFN-γ expression. MOC aspiration before a respiratory challenge with S. pneumoniae led to a decrease in hosts' susceptibility to this pathogen.Conclusions: Thus, in otherwise healthy mice, a single aspiration event with oral commensals is rapidly cleared from the lower airways but induces a prolonged Th17 response that secondarily decreases susceptibility to S. pneumoniae. Translationally, these data implicate an immunoprotective role of episodic microaspiration of oral microbes in the regulation of the lung immune phenotype and mitigation of host susceptibility to infection with lower-airway pathogens.

High-speed Training in a Specific Context in Soccer: Transition Games.

The aims of this study were to compare the load of three tasks designed to train features of soccer: a transition game, a small-sided game with a change of playing area, and a large-sided game. Twenty young elite players performed these tasks. Variables measured were total distance covered (DC), distance covered at 14.0-17.9 km·h-1 (DC 14.0-17.9 km·h-1), distance covered at 18.0-21 km·h-1 (DC 18-21 km·h-1), distance covered > 21 km·h-1 (DC>21 km·h-1), peak speed, accelerations and decelerations > 1.0 and > 2.5 m·s-2, player load, and rate of perceived exertion. Transition games produced greater DC 18-21 km·h-1, DC>21 km·h-1, peak speed and Acc>2.5 m·s-2 than the other drills (p<0.01) and higher DC 14-17.9 km·h-1 (p<0.01), Dec>1 m·s-2 (p<0.05) and Dec>2.5 m·s-2 (p<0.01) than the large-sided game. Both sided games produced more DC (p<0.01), Acc>1 m·s-2 (p<0.01) and player load (p<0.01 and p<0.05, respectively) than the transition game. During the small-sided game, significantly higher DC 14-17.9 km·h-1, DC 18-21 km·h-1 and DC>21 km·h-1 were recorded in comparison with the large-sided game (p<0.01). The studied parameters showed lower variation in the transition game. Coaches could use transition games to train high speed running in counter-attack contexts.

Effects of Different Loading Conditions During Resisted Sprint Training on Sprint Performance.

ABSTRACT: Rodríguez-Rosell, D, Sáez de Villarreal, E, Mora-Custodio, R, Asián-Clemente, JA, Bachero-Mena, B, Loturco, I, and Pareja-Blanco, F. Effects of different loading conditions during resisted sprint training on sprint performance. J Strength Cond Res 36(10): 2725-2732, 2022-The aim of this study was to compare the effects of 5 loading conditions (0, 20, 40, 60, and 80% of body mass [BM]) during weighted sled sprint training on unresisted and resisted sprint performance and jump ability. Sixty physically active men were randomly assigned into 5 groups according to the overload used during sled sprint training: 0% (G0%, n = 12), 20% (G20%, n = 12), 40% (G40%, n = 12), 60% (G60%, n = 12), and 80% BM (G80%, n = 12). Pretraining and post-training assessments included: countermovement jump (CMJ), 30-m sprint without extra load, and 20-m sprint with 20, 40, 60, and 80% BM. All 5 experimental groups trained once a week for a period of 8 weeks completing the same training program (number of sessions, number of bouts, running distance in each sprint, rest intervals between repetitions, and total running distance), but with different sled loads (0, 20, 40, 60, and 80% BM). There was a significant "time × group" interaction for resisted sprint performance at 80% BM condition, where the G40% group attained improvements in performance and G80% worsened. Moreover, G40% increased performance in unresisted and the rest of loading conditions. In addition, G0% and G60% showed statistically significant increases in unresisted sprint performance. No relevant changes were observed in the other experimental groups. All groups showed significant improvements ( p < 0.05-0.001) in CMJ height. Therefore, our findings suggest that resisted sprint training with moderate loads (i.e., 40% BM) may have a positive effect on unresisted and resisted sprint performance.

Quality diet indexes and risk of hepatocellular carcinoma: Findings from the Singapore Chinese Health Study.

There is limited research on the effect of dietary quality on hepatocellular carcinoma (HCC) risk in populations with relatively high risk of HCC. Using data from Singapore Chinese Health Study, a prospective cohort study, of 63 257 Chinese aged 45 to 74, we assessed four diet-quality index (DQI) scores: the Alternative Health Eating Index-2010 (AHEI-2010), Alternate Mediterranean Diet (aMED), Dietary Approaches to Stop Hypertension (DASH) and Heathy Diet Indicator (HDI). We identified 561 incident HCC cases among the cohort participants after a mean of 17.6 years of follow-up. Cox proportional hazard regression model was used to estimate hazard ratio (HR) and 95% confidence interval (CI) for HCC in relation to these DQI scores. Unconditional logistic regression method was used to evaluate the associations between DQIs and HCC risk among a subset of individuals who tested negative for hepatitis B surface antigen (HBsAg). High scores of AHEI-2010, aMED and DASH, representing higher dietary quality, were associated with lower risk of HCC (all Ptrend < .05). Compared with the lowest quartile, HRs (95% CIs) of HCC for the highest quartile of AHEI-2010, aMED and DASH were 0.69 (0.53-0.89), 0.70 (0.52-0.95) and 0.67 (0.51-0.87), respectively. No significant association between HDI and HCC risk was observed. Among HBsAg-negative individuals, similar inverse associations were observed, and the strongest inverse association was for aMED (HRQ4vsQ1 = 0.46, 95% CI: 0.23-0.94, Ptrend = .10). These findings support the notion that adherence to a healthier diet may lower the risk of HCC, suggesting that dietary modification may be an effective approach for primary prevention of HCC.

Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism.

BACKGROUND: Microbiome studies of the lower airways based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short-chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary. METHODS: Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model. We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole-genome shotgun (WGS) and RNA metatranscriptome sequencing. SCFAs were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed. RESULTS: Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome data were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFA levels were compared with WGS and metatranscriptome data. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing. CONCLUSIONS: Functional characterisation of the lower airway microbiota through metatranscriptome data identifies metabolically active organisms capable of producing metabolites with immunomodulatory capacity, such as SCFAs.