Search results for "microbiome"

The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach

2015

AbstractMicrobial communities are ubiquitous in both natural and artificial environments. However, microbial diversity is usually reduced under strong selection pressures, such as those present in habitats rich in recalcitrant or toxic compounds displaying antimicrobial properties. Caffeine is a natural alkaloid present in coffee, tea and soft drinks with well-known antibacterial properties. Here we present the first systematic analysis of coffee machine-associated bacteria. We sampled the coffee waste reservoir of ten different Nespresso machines and conducted a dynamic monitoring of the colonization process in a new machine. Our results reveal the existence of a varied bacterial community…

Mind the gap—deficits in our knowledge of aspects impacting the bioavailability of phytochemicals and their metabolites—a position paper focusing on …

2015

This is an open access article under the terms of the Creative Commons Attribution-Non-Commercial-NoDerivs Licence.-- et al.

Insects’ potential: Understanding the functional role of their gut microbiome

2021

The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as m…

The impact of the gut microbiome in Alzheimer's disease

2020

Abstract Alzheimer's disease is a devastating neurodegenerative disease clearly characterized by loss of synapses, changes in metabolism, and neuronal death in brain tissue. The impact of nutrition and other lifestyle factors on pathomechanisms has been extensively investigated in recent decades. However, one main issue has been out of focus during these research efforts—the human body is not a single entity but provides an ecological niche for a huge number of other organisms, its microbial flora. These microorganisms outnumber the host's genetic pool indisputably. While the human encodes for 30,000 genes, the microbiome of the gastrointestinal tract inherits a multitude of commensal micro…

Midbiotics: conjugative plasmids for genetic engineering of natural gut flora.

2019

ABSTRACT The possibility to modify gut bacterial flora has become an important goal, and various approaches are used to achieve desirable communities. However, the genetic engineering of existing microbes in the gut, which are already compatible with the rest of the community and host immune system, has not received much attention. Here, we discuss and experimentally evaluate the possibility to use modified and mobilizable CRISPR-Cas9-endocing plasmid as a tool to induce changes in bacterial communities. This plasmid system (briefly midbiotic) is delivered from bacterial vector into target bacteria via conjugation. Compared to, for example, bacteriophage-based applications, the benefits of …

Estimating the extent of horizontal gene transfer in metagenomic sequences

2008

Abstract Background Although the extent of horizontal gene transfer (HGT) in complete genomes has been widely studied, its influence in the evolution of natural communities of prokaryotes remains unknown. The availability of metagenomic sequences allows us to address the study of global patterns of prokaryotic evolution in samples from natural communities. However, the methods that have been commonly used for the study of HGT are not suitable for metagenomic samples. Therefore it is important to develop new methods or to adapt existing ones to be used with metagenomic sequences. Results We have created two different methods that are suitable for the study of HGT in metagenomic samples. The …

Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome

2020

Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation—bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that …

Horizontal gene transfer to a defensive symbiont with a reduced genome amongst a multipartite beetle microbiome

2019

ABSTRACTThe loss of functions required for independent life when living within a host gives rise to reduced genomes in obligate bacterial symbionts. Although this phenomenon can be explained by existing evolutionary models, its initiation is not well understood. Here, we describe the microbiome associated with eggs of the beetleLagria villosa, containing multiple bacterial symbionts related toBurkholderia gladioliincluding a reduced-genome symbiont thought to produce the defensive compound lagriamide. We find that the putative lagriamide producer is the only symbiont undergoing genome reduction, and that it has already lost most primary metabolism and DNA repair pathways. The horizontal acq…

Editorial Commentary on “The role of periodontal microorganisms in the pathogenesis of myocardial infarction. From PCR techniques to microbiome seque…

2021

Co-factors, Microbes, and Immunogenetics in Celiac Disease to Guide Novel Approaches for Diagnosis and Treatment.

2021

Celiac disease (CeD) is a frequent immune-mediated disease that affects not only the small intestine but also many extraintestinal sites. The role of gluten proteins as dietary triggers, HLA-DQ2 or -DQ8 as major necessary genetic predisposition, and tissue transglutaminase (TG2) as mechanistically involved autoantigen, are unique features of CeD. Recent research implicates many cofactors working in synergism with these key triggers, including the intestinal microbiota and their metabolites, nongluten dietary triggers, intestinal barrier defects, novel immune cell phenotypes, and mediators and cytokines. In addition, apart from HLA-DQ2 and -DQ8, multiple and complex predisposing genetic fact…