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

Belforte, Fiorella S.; Fernandez, Natalie; Monzón, Francisco Tonín; Rosso, Ayelén Daiana; Quesada, Sofía; Cimolai, María Cecilia; Millán, Andrea; Cerrone, Gloria Edith; Frechtel, Gustavo Daniel; Burcelin, Rémy; Leskow, Federico Coluccio; Steinhardt, Alberto Penas

doi:10.3389/fmicb.2019.00965

Cited by 9 publications

(13 citation statements)

References 56 publications

(64 reference statements)

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“…This last phylum had been previously reported within the general population of Buenos Aires (Argentina) and Santiago de Chile [18,22] . There are several studies where Akkermansia municiphila…”

Section: Regarding Relative Abundance At Phylum Level Our Results Fosupporting

confidence: 63%

“…Each participant was given a written protocol for sample collection, which considered the introduction of approximately 5g of stool into a sterile wide-mouth tube containing a teaspoon in the lid. DMSO/EDTA/saturated sodium chloride buffer was used to preserve the samples at both room and subzero temperatures, preventing freezing and cell damage as described [22,29] . The samples were aliquoted and stored at -80°C until use.…”

Section: Sample Collection and Dna Extractionmentioning

confidence: 99%

“…This could improve sampling limitations and consider intestinal mucosa metabolism within our local environmental factors, allowing a better understanding of the role of the gut dysbiosis in these chronic diseases of unknown etiology. In this sense, several publications mention the importance of knowing the microbiome of each region, since it is conditioned by intrinsic local factors [22,77] .…”

mentioning

confidence: 99%

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New insights in Ulcerative Colitis Associated Gut Microbiota in South American Population: Akkermansia and Collinsella, two distinctive genera found in Argentine subjects

Aguilera

Quesada

et al. 2020

Preprint

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Background Globally, ulcerative colitis (UC) is the most common form of intestinal inflammation, which is believed to be the result of a deregulated immune system response to commensal microbiota in a genetically susceptible host. Multicellular organisms rely heavily on their commensal symbiotic microbiota, whose composition is closely related to intrinsic local characteristics and regulated or modified by environmental factors. In the present study we aim to describe the unknown gut microbiota of patients with UC in comparison with healthy individuals in order to find novel biomarkers for UC in our region. Methods We evaluated 46 individuals, 26 healthy non-UC controls and 20 UC patients, from the metropolitan area of Buenos Aires (BA), Argentina. Clinical features, biochemical tests and anthropometric measurements were determined. Fecal samples were collected and DNA was extracted for microbiota analysis. The hypervariable regions V3-V4 of the bacterial 16SR gene were sequenced using a MiSeq platform and sequences were analyzed using the QIIME2 environment. In addition, we looked for differential functional pathways using PICRUSt and compared the performance of three machine learning models to discriminate the studied individuals, using taxa and functional annotations. Results All UC patients were under clinical treatment with 70% of individuals in remission. We found no significant differences in gut microbiota richness or evenness between UC patients and non-UC controls (alpha diversity). Remarcably, microbial compositional structure within groups (beta diversity) showed differences: At the phylum level, Verrucomicrobia was overrepresented in controls while Actinobacteria was distinctive of UC patients; At the genus level Bacteroides and Akkermancia were significantly more abundant among controls while Eubacterium and Collinsella in UC patients. In addition, our results showed that carbohydrates metabolism was preponderant in UC patients, not observing a distinctive biochemical pathway for the healthy non-UC controls. Finally, in order to define a robust classifying method in our population, we evaluated the capability of three machine learning models to classify individuals. Our results reinforced the idea of functional compensation in microbiome communities, as models that used KEGG orthologs annotations had better capabilities than taxonomy to distinguish UC patients. Conclusions Our study provides new knowledge on the differences and similarities of the gut microbiota of UC patients as compared to non-UC controls of our population. This allows not only the association of local changes in gut microbial diversity with the pathology process, but also the future development of personalized nutritional and pharmacological therapies through the use of omic strategies describing the metagenomic profiles of the Argentine population.

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Section: Regarding Relative Abundance At Phylum Level Our Results Fosupporting

confidence: 63%

Section: Sample Collection and Dna Extractionmentioning

confidence: 99%

mentioning

confidence: 99%

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New insights in Ulcerative Colitis Associated Gut Microbiota in South American Population: Akkermansia and Collinsella, two distinctive genera found in Argentine subjects

Aguilera

Quesada

et al. 2020

Preprint

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“…There is evidence that age, diet, geographical location, genetics and antibiotics, among other factors, influence gut microbiota 72,73 . We selected unrelated controls matched by sex, age and BMI to moderate-to-severe psoriasis patients, living in the same area and with a similar diet in order to reduce those confounding factors.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index

Dei-Cas

Giliberto

Luce

et al. 2020

Sci Rep

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psoriasis is an immune-mediated skin disorder. imbalance of gut microbial populations has been implicated in many diseases. We aimed to investigate whether there were differences in gut microbiota in psoriasis patients vs non-psoriasis controls and between psoriasis severity groups. 55 psoriasis patients and 27 controls were included. V3-V4 regions of the 16S rRNA gene of fecal samples were analyzed using Illumina MiSeq. Bioinformatic analysis was performed. We found changes in gut microbiome composition depending on their psoriasis status as determined by weighted unifrac (p < 0.05), in particular an increase in Firmicutes and depletion of Bacteroidetes in psoriasis patients. Additionally, the Faecalibacterium and Blautia genus were higher in psoriasis patients while Bacteroides and Paraprevotella in non-psoriasis controls (p < 0.05, LDA score > 2). Moderate-to-severe psoriasis patients had lower biodiversity than mild psoriatic patients (p = 0.049). No differences for beta-diversity were found. We developed a Psoriasis-Microbiota Index (PMI), which discriminated among psoriasis patients and controls with sensitivity: 0.78 and specificity: 0.79. Furthermore, we performed a meta-analysis with published data to validate this index. We demonstrated gut dysbiosis in psoriasis patients, suggesting a role in psoriasis pathophysiology. Furthermore, we developed a PMI with the potential to discriminate between psoriasis patients and controls across different populations, which could be used as a biomarker in the clinical practice. Psoriasis is a chronic, immune-mediated inflammatory skin disease. It ranges in severity from a few scattered red, scaly plaques to involvement of almost the entire body surface 1. Psoriasis is estimated to affect about 2-4% of the population in western countries, causes considerable psychosocial disability and has a major impact on patients' quality of life 2,3. Skin lesions are characterized by angiogenesis, an inflammatory reaction with recruitment of T cells into the skin, hyperproliferation of keratinocytes and altered epidermal differentiation 4. Genetic and environmental factors are implicated in psoriasis, although, the exact etiology of the disease is not fully understood 5,6 .

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“…This is in agreement with a previous study, in which country of origin accounted for a similar amount of variation ( R 2 = 22%) [ 50 ]. Additionally, countries within continents also showed greater microbial similarity [ 51 , 52 ]. Inter-continent differences in microbiome structure were likely a consequence of the inverse Prevotella to Bacteroides ratio of Asian and South American samples.…”

Section: Discussionmentioning

confidence: 99%

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries

et al. 2021

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Background The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport. Here, we aimed (1) to establish a broad representation of diverse developing countries (Argentina, Chile, India, and Vietnam); (2) to validate a ‘resource-light’ sample-collection protocol translatable in these settings using guaiac faecal occult blood test (gFOBT) cards stored and, importantly, shipped internationally at room temperature; (3) to perform initial profiling of the collective CRC-associated microbiome of these developing countries; and (4) to compare this quantitatively with established CRC biomarkers from developed countries. Methods We assessed the effect of international storage and transport at room temperature by replicating gFOBT from five UK volunteers, storing two in the UK, and sending replicates to institutes in the four countries. Next, to determine the effect of prolonged UK storage, DNA extraction replicates for a subset of samples were performed up to 252 days apart. To profile the CRC-associated microbiome of developing countries, gFOBT were collected from 41 treatment-naïve CRC patients and 40 non-CRC controls from across the four institutes, and V4 16S rRNA gene sequencing was performed. Finally, we constructed a random forest (RF) model that was trained and tested against existing datasets from developed countries. Results The microbiome was stably assayed when samples were stored/transported at room temperature and after prolonged UK storage. Large-scale microbiome structure was separated by country and continent, with a smaller effect from CRC. Importantly, the RF model performed similarly to models trained using external datasets and identified similar taxa of importance (Parvimonas, Peptostreptococcus, Fusobacterium, Alistipes, and Escherichia). Conclusions This study demonstrates that gFOBT, stored and transported at room temperature, represents a suitable method of faecal sample collection for amplicon-based microbiome biomarkers in developing countries and suggests a CRC-faecal microbiome association that is consistent between developed and developing countries.

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

Cited by 9 publications

References 56 publications

New insights in Ulcerative Colitis Associated Gut Microbiota in South American Population: Akkermansia and Collinsella, two distinctive genera found in Argentine subjects

New insights in Ulcerative Colitis Associated Gut Microbiota in South American Population: Akkermansia and Collinsella, two distinctive genera found in Argentine subjects

Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries

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