scholarly journals Metanacentome: A genomic methodology for the study of nascent metatranscription of the microbiome

Author(s):  
Daniel A. Medina

The gut microbiota has been shown to have an important influence on host health. Microbial composition of the gut microbiota is modulated by diet and human habits. The composition of human gut microbiota changes with age; and alterations in this composition may influence human health. It has been reported that microbiota composition of each individual is stable across the adult life, but it may varies between individuals. Moreover, human gut microbiota composition differs across geography, according to host genetics, dietary habits, age, ethnic origin, geographic location and lifestyle. Nevertheless, gene composition or functional capacity is highly conserved across individuals, phenomenon known as functional redundancy. Although metatranscriptomics can study the mature mRNA from a microbiome sample, it is impossible identify who bacteria is actively transcribing the genes who drives the molecular expression. The use of genome-wide methodologies to study the active mRNA synthesis could be useful to identify the bacterial population who drives gene expression in microbiome environment.

2019 ◽  
Author(s):  
Daniel A. Medina

The gut microbiota has been shown to have an important influence on host health. It has been reported that microbiota composition of each individual is stable across the adult life, but it may varies between individuals. Moreover, human gut microbiota composition differs across geography, according to host genetics, dietary habits, age, ethnic origin, geographic location and lifestyle. Nevertheless, gene composition or functional capacity is highly conserved across individuals, phenomenon known as functional redundancy. Although metatranscriptomics have the potential of study the mature mRNA from a microbiome sample, it is not easy to identify which bacteria is actively transcribing the genes who drives the molecular expression. The use of genome-wide methodologies to study the active mRNA synthesis seem to be useful to identify the bacterias who drives gene expression in microbiota environment.


2019 ◽  
Author(s):  
Daniel A. Medina

The gut microbiota has been shown to have an important influence on host health. It has been reported that microbiota composition of each individual is stable across the adult life, but it may varies between individuals. Moreover, human gut microbiota composition differs across geography, according to host genetics, dietary habits, age, ethnic origin, geographic location and lifestyle. Nevertheless, gene composition or functional capacity is highly conserved across individuals, phenomenon known as functional redundancy. Although metatranscriptomics have the potential of study the mature mRNA from a microbiome sample, it is not easy to identify which bacteria is actively transcribing the genes who drives the molecular expression. The use of genome-wide methodologies to study the active mRNA synthesis seem to be useful to identify the bacterias who drives gene expression in microbiota environment.


2019 ◽  
Author(s):  
Robin Mesnage ◽  
Franziska Grundler ◽  
Andreas Schwiertz ◽  
Yvon Le Maho ◽  
Françoise Wilhelmi de Toledo

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander Koliada ◽  
Vladislav Moseiko ◽  
Mariana Romanenko ◽  
Oleh Lushchak ◽  
Nadiia Kryzhanovska ◽  
...  

Abstract Background Evidence was previously provided for sex-related differences in the human gut microbiota composition, and sex-specific discrepancy in hormonal profiles was proposed as a main determinant of these differences. On the basis of these findings, the assumption was made on the role of microbiota in the sexual dimorphism of human diseases. To date, sex differences in fecal microbiota were demonstrated primarily at lower taxonomic levels, whereas phylum-level differences between sexes were reported in few studies only. In the present population-based cross-sectional research, sex differences in the phylum-level human gut microbiota composition were identified in a large (total n = 2301) sample of relatively healthy individuals from Ukraine. Results Relative abundances of Firmicutes and Actinobacteria, as determined by qRT-PCR, were found to be significantly increased, while that of Bacteroidetes was significantly decreased in females compared to males. The Firmicutes to Bacteroidetes (F/B) ratio was significantly increased in females compared to males. Females had 31 % higher odds of having F/B ratio more than 1 than males. This trend was evident in all age groups. The difference between sexes was even more pronounced in the elder individuals (50+): in this age group, female participants had 56 % higher odds of having F/B ratio > 1 than the male ones. Conclusions In conclusion, sex-specific differences in the phylum-level intestinal microbiota composition were observed in the Ukraine population. The F/B ratio was significantly increased in females compared to males. Further investigation is needed to draw strong conclusions regarding the mechanistic basis for sex-specific differences in the gut microbiota composition and regarding the role of these differences in the initiation and progression of human chronic diseases.


2021 ◽  
Vol 84 ◽  
pp. 104596
Author(s):  
Benjamín Vázquez-Rodríguez ◽  
Liliana Santos-Zea ◽  
Erick Heredia-Olea ◽  
Laura Acevedo-Pacheco ◽  
Arlette Santacruz ◽  
...  

2021 ◽  
Vol 9 (8) ◽  
pp. 1763
Author(s):  
Veronica Di Cristanziano ◽  
Fedja Farowski ◽  
Federica Berrilli ◽  
Maristella Santoro ◽  
David Di Cave ◽  
...  

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d’Ivoire. Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays. Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected. Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis.


2021 ◽  
Vol 70 (7) ◽  
pp. 5-10
Author(s):  
K.A. Aitbaev ◽  
I.T. Murkamilov ◽  
V.V. Fomin ◽  
Zh.A. Murkamilova ◽  
I.O. Kudaibergenova ◽  
...  

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
T. M. Cantu-Jungles ◽  
B. R. Hamaker

ABSTRACT Dietary fibers can be utilized to shape the human gut microbiota. However, the outcomes from most dietary fibers currently used as prebiotics are a result of competition between microbes with overlapping abilities to utilize these fibers. Thus, divergent fiber responses are observed across individuals harboring distinct microbial communities. Here, we propose that dietary fibers can be classified hierarchically according to their specificity toward gut microbes. Highly specific fibers harbor chemical and physical characteristics that allow them to be utilized by only a narrow group of bacteria within the gut, reducing competition for that substrate. The use of such fibers as prebiotics targeted to specific microbes would result in predictable shifts independent of the background microbial composition.


2020 ◽  
Vol 79 (OCE2) ◽  
Author(s):  
Ilaria Carafa ◽  
Domenico Masuero ◽  
Urska Vrhovsek ◽  
Giovanni Bittante ◽  
Elena Franciosi ◽  
...  

AbstractConjugated linoleic acids (CLAs) show a number of putative health-promoting activities including anti-carcinogenic, anti-adipogenic, anti-diabetogenic, anti-inflammatory and antioxidant actions. CLAs are naturally produced by ruminal bacteria and several studies demonstrate that various lactobacilli and bifidobacteria are also able to produce CLAs in vitro from linoleic acid (LA). However, the ability of the human gut microbiota to produce CLA is less extensively studied. Our hypothesis is that the human gut microbiota is able to convert LA to CLA, and that the readily fermentable fiber inulin would positively modulate the growth of CLA-producing bacteria and, consequently increase the CLA content in the intestine.The capability of the faecal microbiota from five healthy donors to produce CLA was tested in anaerobic batch cultures for 48 hours at pH 5.5 and 6.5. Test treatments were linoleic acid (LA; 1 mg/mL) + bovine serum albumin (BSA; 0.2 mg/mL), and LA (1 mg/mL) + BSA (0.2 mg/mL) + inulin (1%, w/v) compared to a control BSA (0.2 mg/mL) fermentation. The microbial composition was analyzed 0, 24 and 48 hours after starting the fermentation by 16S rRNA gene Illumina MiSeq sequencing (V3-V4 region). CLAs were quantified by Ultra performance liquid chromatography - tandem mass spectrometer (UPLC-MS/MS) and bi-dimensional gas chromatography (GC x GC).The inclusion of LA + BSA + inulin at pH 5.5 significantly increased the relative abundance of Collinsella aerofaciens (p < 0.05), and tended to increase the relative abundance of bifidobacteria. LA + BSA + inulin at both pH 5.5 and 6.5 reduced the relative abundance of Parabacteroides, Bilophila, Clostridia and Enterobacteriaceae (p < 0.05). The concentration of CLA, in particular the isomer cis9,trans11 C18:2, was significantly higher in the LA + BSA + inulin group at pH 5.5 after 24 and 48 hours fermentation.The data show that the treatment LA + BSA + inulin at pH 5.5 induce substantial changes in microbiota composition, including bifidogenesis and CLA production in a human intestinal microbiota model. The changes of relative abundance detected are consistent with changes in gut bacteria previously linked to human health. Collinsella aerofaciens has been reported for reducing bloating, in particular in subjects suffering from irritable bowel syndrome, while Clostridia, Bilophila and Enterobacteriaceae causes human infections. In addition, the increase of bifidobacteria and LAB, which have previously been shown in vitro to produce CLA, may also be involved in CLA production under simulated cecal microbiome. These preclinical observations warrant confirmation in suitably designed animal and human mechanistic studies.


Nutrients ◽  
2017 ◽  
Vol 9 (6) ◽  
pp. 533 ◽  
Author(s):  
Athanasios Koutsos ◽  
Maria Lima ◽  
Lorenza Conterno ◽  
Mattia Gasperotti ◽  
Martina Bianchi ◽  
...  

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