Integrated analysis of the transcriptome and its interaction with the metabolome in metabolic associated fatty liver disease: Gut microbiome signatures, correlation networks, and effect of PNPLA3 genotype.

Interactions between communities of the gut microbiome and with the host could affect the onset and progression of metabolic associated fatty liver disease (MAFLD), and can be useful as new diagnostic and prognostic biomarkers. In this study, we performed a multi-omics approach to unravel gut microbiome signatures from 32 biopsy-proven patients (10 simple steatosis -SS- and 22 steatohepatitis -SH-) and 19 healthy volunteers (HV). Human and microbial transcripts were differentially identified between groups (MAFLD vs. HV/SH vs. SS), and analyzed for weighted correlation networks together with previously detected metabolites from the same set of samples. We observed that expression of Desulfobacteraceae bacterium, methanogenic archaea, Mushu phage, opportunistic pathogenic fungi Fusarium proliferatum and Candida sorbophila, protozoa Blastocystis spp. and Fonticula alba were upregulated in MAFLD and SH. Desulfobacteraceae bacterium and Mushu phage were hub species in the onset of MAFLD, whereas the activity of Fonticula alba, Faecalibacterium prausnitzii, and Mushu phage act as key regulators of the progression to SH. A combination of clinical, metabolomic, and transcriptomic parameters showed the highest predictive capacity for MAFLD and SH (AUC = 0.96). In conclusion, faecal microbiome markers from several community members contribute to the switch in signatures characteristic of MAFLD and its progression towards SH.

Plasma and stool metabolomics to identify microbiota derived-biomarkers of metabolic dysfunction-associated fatty liver disease: effect of PNPLA3 genotype.

INTRODUCTION: Non-invasive biomarkers are needed for metabolic dysfunction-associated fatty liver disease (MAFLD), especially for patients at risk of disease progression in high-prevalence areas. The microbiota and its metabolites represent a niche for MAFLD biomarker discovery. However, studies are not reproducible as the microbiota is variable. OBJECTIVES: We aimed to identify microbiota-derived metabolomic biomarkers that may contribute to the higher MAFLD prevalence and different disease severity in Latin America, where data is scarce. METHODS: We compared the plasma and stool metabolomes, gene patatin-like phospholipase domain-containing 3 (PNPLA3) rs738409 single nucleotide polymorphism (SNP), diet, demographic and clinical data of 33 patients (12 simple steatosis and 21 steatohepatitis) and 19 healthy volunteers (HV). The potential predictive utility of the identified biomarkers for MAFLD diagnosis and progression was evaluated by logistic regression modelling and ROC curves. RESULTS: Twenty-four (22 in plasma and 2 in stool) out of 424 metabolites differed among groups. Plasma triglyceride (TG) levels were higher among MAFLD patients, whereas plasma phosphatidylcholine (PC) and lysoPC levels were lower among HV. The PNPLA3 risk genotype was related to higher plasma levels of eicosenoic acid or fatty acid 20:1 (FA(20:1)). Body mass index and plasma levels of PCaaC24:0, FA(20:1) and TG (16:1_34:1) showed the best AUROC for MAFLD diagnosis, whereas steatosis and steatohepatitis could be discriminated with plasma levels of PCaaC24:0 and PCaeC40:1. CONCLUSION: This study identified for the first time MAFLD potential non-invasive biomarkers in a Latin American population. The association of PNPLA3 genotype with FA(20:1) suggests a novel metabolic pathway influencing MAFLD pathogenesis.

Omics-based biomarkers as useful tools in metabolic dysfunction-associated steatotic liver disease clinical practice: How far are we?

Unmet needs exist in metabolic dysfunction-associated steatotic liver disease (MASLD) risk stratification. Our ability to identify patients with MASLD with advanced fibrosis and at higher risk for adverse outcomes is still limited. Incorporating novel biomarkers could represent a meaningful improvement to current risk predictors. With this aim, omics technologies have revolutionized the process of MASLD biomarker discovery over the past decades. While the research in this field is thriving, much of the publication has been haphazard, often using single-omics data and specimen sets of convenience, with many identified candidate biomarkers but lacking clinical validation and utility. If we incorporate these biomarkers to direct patients' management, it should be considered that the roadmap for translating a newly discovered omics-based signature to an actual, analytically valid test useful in MASLD clinical practice is rigorous and, therefore, not easily accomplished. This article presents an overview of this area's current state, the conceivable opportunities and challenges of omics-based laboratory diagnostics, and a roadmap for improving MASLD biomarker research.

A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic.

The COVID-19 pandemic poses a great challenge to global public health. The extraordinary daily use of household disinfectants and cleaning products, social distancing and the loss of everyday situations that allow contact between individuals, have a direct impact on the transfer of microorganisms within the population. Together, these changes, in addition to those that occur in eating habits, can affect the composition and diversity of the gut microbiota. A two-time point analysis of the fecal microbiota of 23 Metropolitan Buenos Aires (BA) inhabitants was carried out, to compare pre-pandemic data and its variation during preventive and compulsory social isolation (PCSI) in 2020. To this end, 23 healthy subjects, who were previously studied by our group in 2016, were recruited for a second time during the COVID-19 pandemic, and stool samples were collected from each subject at each time point (n = 46). The hypervariable region V3-V4 of the 16S rRNA gene was high-throughput sequenced. We found significant differences in the estimated number of observed features (p < 0.001), Shannon entropy index (p = 0.026) and in Faith phylogenetic diversity (p < 0.001) between pre-pandemic group (PPG) vs. pandemic group (PG), being significantly lower in the PG. Although no strong change was observed in the core microbiota between the groups in this study, a significant decrease was observed during PCSI in the phylum Verrucomicrobia, which contributes to intestinal health and glucose homeostasis. Microbial community structure (beta diversity) was also compared between PPG and PG. The differences observed in the microbiota structure by unweighted UniFrac PCoA could be explained by six differential abundant genera that were absent during PCSI. Furthermore, putative functional genes prediction using PICRUSt infers a smaller predicted prevalence of genes in the intestinal tryptophan, glycine-betaine, taurine, benzoate degradation, as well as in the synthesis of vitamin B12 during PCSI. This data supports the hypothesis that the microbiome of the inhabitants of BA changed in the context of isolation during PCSI. Therefore, these results could increase the knowledge necessary to propose strategic nutraceutical, functional food, probiotics or similar interventions that contribute to improving public health in the post-pandemic era.

The genetic variability of hepatitis B virus subgenotype F1b precore/core gene is related to the outcome of the acute infection.

AIM: To assess the association of viral and host genetic variability with the outcome of acute infection with hepatitis B virus subgenotype F1b (HBV/F1b). METHODS: The cohort consisted of 26 patients with acute HBV/F1b infection who exhibit different outcomes: spontaneous resolution (n = 10), progression to chronic hepatitis (n = 10) and acute liver failure (n = 6). HLA SNPs (rs3077, rs9277542, rs2856718 and rs7453920) were determined. The S gene and core promoter/precore/core region were direct sequenced, and this latter region was also ultra-deep sequenced. Mean number of mutations, mutation rate, Shannon entropy, positive selection sites and mutational patterns of quasispecies were compared between groups. RESULTS: HLA SNPs were associated with spontaneous resolution or progression to chronic hepatitis, but not with the development of acute liver failure. The mean number of mutations in the S gene was similar among the three groups. Patients with spontaneous resolution had the lowest number of mutations, mutation rates and Shannon entropy values in the precore/core compared to the other two groups. Ten positive selection sites mapped on HLA-restricted epitopes were related to progression to chronic hepatitis and acute liver failure. Mutations T1753C, A1762T, G1764A, C1766T, T1768A G1896A, G2092T and T2107C were associated with acute liver failure and progression to chronic hepatitis. CONCLUSION: Highly heterogeneous and complex HBV precore/core carrying specific point mutations, combined with the host HLA background, were associated with a worse clinical outcome of acute HBV/F1b infection.

ESTUDIO METAGENÓMICO DE LA MICROBIOTA INTESTINAL EN PACIENTES CON OBESIDAD MÓRBIDA SOMETIDOS A CIRUGÍA BARIÁTRICA / METAGENOMIC STUDY OF THE INTESTINAL MICROBIOTA IN PATIENTS WITH MORBID OBESITY UNDERGOING BARIATRIC SURGERY

Introducción: La cirugía bariátrica (CB) es un tratamiento quirúrgico de la obesidad, cuyo objetivo es lograr el descenso de peso, de masa grasa y alcanzar un impacto metabólico a largo plazo. Se ha observado que ciertos pacientes no responden tan efectivamente a la cirugía, teniendo un descenso de peso inefectivo o recuperando peso tardíamente, y los mecanismos por lo que esto ocurre aún no están bien caracterizados. La microbiota intestinal tiene un rol esencial en varios de los procesos metabólicos asociados a la obesidad. El objetivo de este estudio fue caracterizar el metagenoma intestinal de pacientes candidatos para CB y otros que fueron operados, así como también evaluar las diferencias entre aquellos pacientes que tuvieron un resultado exitoso de la CB y los que no. Material y método: Se extrajo el ADN de 200 mg de heces de pacientes que cumplen criterios de CB, divididos en 3 grupos, basal (preoperatorio), 12 meses y más de 24 meses postoperatorios, con el fin de estudiar y comparar el perfil taxonómico de las comunidades bacterianas de la microbiota intestinal. Resultados: Mientras que la riqueza específica de los grupos de estudio no presentó diferencias significativas, la diversidad beta, que considera las abundancias relativas de los miembros de las comunidades bacterianas estudiadas, evidenció una composición global significativamente diferente entre los grupos de estudio. Sin embargo, nuestro análisis no identificó taxones específicos que pudieran dar explicación a la distinta evolución postoperatoria de los pacientes. Discusión: En la estructura de las comunidades microbianas, se observaron diferencias numéricas entre los grupos en cuanto a la riqueza y abundancia de taxones así como la comparación cuanti y cualitativa. Esta última presentó significativa disimilitud. Los resultados muestran que la principal diferencia entre los grupos de estudio se basó en la abundancia relativa de los gérmenes, cuyo estudio integral podría revelar patrones más consistentes y significativos vinculados a los mecanismos de respuesta terapéutica en sujetos sometidos a CB

Introduction: Bariatric surgery (BS) is a surgical treatment of obesity, which aims to achieve weight loss, fat mass loss and achieve a long-term metabolic impact. It has been observed that certain patients do not respond as effectively to surgery, having ineffective weight loss or regaining weight late, and the mechanisms by which this occurs are not yet well characterized. The intestinal microbiota plays an essential role in several of the metabolic processes associated with obesity. The objective of our study was to characterize the intestinal metagenome of candidate patients for CB and others who underwent surgery, as well as evaluate the differences between those patients who had a successful outcome from CB and those who did not. Material and method: DNA was extracted from 200 mg of feces from patients who met the criteria for surgical indication divided into 3 groups, baseline (preoperative), 12 months and more than 24 months postoperatively, in order to analyze and compare the taxonomic profile of the bacterial communities of the intestinal microbiota. Results: While the specific richness of the study groups did not present significant differences, beta diversity, which considers the relative abundances of the members of the bacterial communities studied, showed a significantly different global composition between the study groups. Nevertheless, our study did not identify specific taxa that could explain the different postoperative evolution of the patients. Discussion: In the structure of the microbial communities, numerical differences were observed between the groups in terms of the richness and abundance of taxa as well as the quantitative and qualitative comparison. The latter evidenced significant dissimilarity. The results show that the main difference between the study groups was based on the relative abundance of the germs, whose comprehensive study could reveal more consistent and significant patterns linked to the therapeutic response mechanisms in subjects subjected to CB. Bariatric surgery (BS) is a surgical treatment of obesity, whose objective is to achieve weight loss, fat mass and achieve a longterm metabolic impact. However, it has been observed that certain patients do not respond as effectively to surgery, having ineffective weight loss or late weight regain, and the mechanisms by which this occurs are not yet well characterized. The intestinal microbiota plays an essential role in several of the metabolic processes associated with obesity. The aim of this study was to characterize the intestinal metagenome of patients who will and who underwent BS, as well as to assess the differences between those patients who had a successful BS outcome and those who did not. Our results did not identify specific taxa that could explain the different evolution of the patients. While the specific richness of the study groups did not present significant differences, the beta diversity, which considers the relative abundances of the members of the studied bacterial communities, showed a significantly different global composition between the study groups