Integrative analysis of systemic lupus erythematosus biomarkers: Role of fecal hsa-mir-223-3p and gut microbiota in transkingdom dynamics.

Systemic lupus erythematosus (SLE) involves a florid set of clinical manifestations whose autoreactive origin is characterized by an overactivation of the immune system and the production of a large number of autoantibodies. Because it is a complex pathology with an inflammatory component, its pathogenesis is not yet fully understood, assuming both genetic and environmental predisposing factors. Currently, it is known that the role of the human microbiome is crucial in maintaining the transkingdom balance between commensal microorganisms and the immune system. In the present work we study the intestinal microbiota of Argentine patients with different stages of SLE receiving or not different treatments. Microbiota composition and fecal miRNAs were assessed by 16 S sequencing and qPCR. hsa-miR-223-3p, a miRNA involved in several inflammation regulation pathways, was found underexpressed in SLE patients without immunosuppressive treatment. In terms of microbiota there were clear differences in population structure (Weighted and Unweighted Unifrac distances, p-value <0.05) and core microbiome between cases and controls. In addition, Collinsella, Bifidobacterium, Streptococcus genera and aromatics degradation metabolisms were overrepresented in the SLE group. Medical treatment was also determinant as several microbial metabolic pathways were influenced by immunosuppressive therapy. Particularly, allantoin degradation metabolism was differentially expressed in the group of patients receiving immunosuppressants. Finally, we performed a logistic regression model (LASSO: least absolute shrinkage and selection operator) considering the expression levels of the fecal hsa-miR223-3p; the core microbiota; the differentially abundant bacterial taxa and the differentially abundant metabolic pathways (p<0.05). The model predicted that SLE patients could be associated with greater relative abundance of the formaldehyde oxidation pathway (RUMP_PWY). On the contrary, the preponderance of the ketodeoxyoctonate (Kdo) biosynthesis and activation route (PWY_1269) and the genera Lachnospiraceae_UCG_004, Lachnospira, Victivallis and UCG_003 (genus belonging to the family Oscillospiraceae of the class Clostridia) were associated with a control phenotype. Overall, the present work could contribute to the development of integral diagnostic tools for the comprehensive phenotyping of patients with SLE. In this sense, studying the commensal microbial profile and possible pathobionts associated with SLE in our population proposes more effective and precise strategies to explore possible treatments based on the microbiota of SLE patients.

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

Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context.

Inflammatory bowel disease (IBD) is the most common form of intestinal inflammation associated with a dysregulated immune system response to the commensal microbiota in a genetically susceptible host. IBD includes ulcerative colitis (UC) and Crohn's disease (CD), both of which are remarkably heterogeneous in their clinical presentation and response to treatment. This translates into a notable diagnostic challenge, especially in underdeveloped countries where IBD is on the rise and access to diagnosis or treatment is not always accessible for chronic diseases. The present work characterized, for the first time in our region, epigenetic biomarkers and gut microbial profiles associated with UC and CD patients in the Buenos Aires Metropolitan area and revealed differences between non-IBD controls and IBD patients. General metabolic functions associated with the gut microbiota, as well as core microorganisms within groups, were also analyzed. Additionally, the gut microbiota analysis was integrated with relevant clinical, biochemical and epigenetic markers considered in the follow-up of patients with IBD, with the aim of generating more powerful diagnostic tools to discriminate phenotypes. Overall, our study provides new insights into data analysis algorithms to promote comprehensive phenotyping tools using quantitative and qualitative analysis in a transkingdom interactions network context.

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.

Getting to Know the Gut Microbial Diversity of Metropolitan Buenos Aires Inhabitants.

In recent years, the field of immunology has been revolutionized by the growing understanding of the fundamental role of microbiota in the immune system function. The immune system has evolved to maintain a symbiotic relationship with these microbes. The aim of our study was to know in depth the uncharacterized metagenome of the Buenos Aires (BA) city population and its metropolitan area, being the second most populated agglomeration in the southern hemisphere. For this purpose, we evaluated 30 individuals (age: 35.23 ± 8.26 years and BMI: 23.91 ± 3.4 kg/m2), from the general population of BA. The hypervariable regions V3-V4 of the bacterial 16S gene was sequenced by MiSeq-Illumina system, obtaining 47526 ± 4718 sequences/sample. The dominant phyla were Bacteroidetes, Firmicutes, Proteobacteria, Verrucomicrobia, and Actinobacteria. Additionally, we compared the microbiota of BA with other westernized populations (Santiago de Chile, Rosario-Argentina, United States-Human-microbiome-project, Bologna-Italy) and the Hadza population of hunter-gatherers. The unweighted UniFrac clustered together all westernized populations, leaving the hunter-gatherer population from Hadza out. In particular, Santiago de Chile's population turns out to be the closest to BA's, principally due to the presence of Verrucomicrobiales of the genus Akkermansia. These microorganisms have been proposed as a hallmark of a healthy gut. Finally, westernized populations showed more abundant metabolism related KEEG pathways than hunter-gatherers, including carbohydrate metabolism (amino sugar and nucleotide sugar metabolism), amino acid metabolism (alanine, aspartate and glutamate metabolism), lipid metabolism, biosynthesis of secondary metabolites, and sulfur metabolism. These findings contribute to promote research and comparison of the microbiome in different human populations, in order to develop more efficient therapeutic strategies for the restoration of a healthy dialogue between host and environment.