Metagenomics--the key to the uncultured microbes.

Institut für Mikrobiologie und Genetik, Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany.
Current Opinion in Microbiology (Impact Factor: 7.22). 11/2004; 7(5):492-8. DOI: 10.1016/j.mib.2004.08.002
Source: PubMed

ABSTRACT It is widely accepted that up to 99.8% of the microbes present in many environments are not readily culturable. 'Metagenome technology' tries to overcome this bottleneck by developing and using culture-independent approaches. From the outset, metagenome-based approaches have led to the accumulation of an increasing number of DNA sequences, but until this time the sequences retrieved have been those of uncultured microbes. These genomic sequences are currently exploited for novel biotechnological and pharmaceutical applications and to increase our knowledge on microbial ecology and physiology of these microbes. Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today.


Available from: Wolfgang R Streit, May 28, 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Commercial poultry is an important agricultural industry worldwide. Although dense living conditions and large flocks increase meat and egg production, they also increase the risk of disease outbreaks and zoonoses. Current pathogen identification methods mostly rely on culture-dependent techniques and, therefore, are limited to a very small number of bacteria present in the environment. Next Generation Sequencing allows for culture-independent characterization of lower respiratory microbiome of birds including the identification of novel commensals and potentially emerging pathogens. In this study, we collected tracheo-bronchoalveolar lavage of 14 birds raised at 3 different farms in the Punjab province of Pakistan. To characterize the lower respiratory microbiome of these birds, we sequenced hyper-variable regions of the 16S ribosomal subunit gene. Although dominated by bacteria belonging to a small number of taxonomic classifications, the lower respiratory microbiome from each farm was far more diverse and novel than previously known. The differences in microbiome among farms suggest that inter-farm differences affect the microbiome of birds more than breed, geographic location, or management system. The presence of potential and known pathogens in genetically similar specialty breeds of chickens kept at unnaturally high densities and under variable conditions presents an extraordinary opportunity for the selection of highly pathogenic bacteria. In some instances, opportunistic respiratory pathogens were observed in apparently healthy birds. Understanding and monitoring the respiratory microbiome of such populations may allow the early detection of future disease threats. © 2015 Poultry Science Association Inc.
    Poultry Science 02/2015; DOI:10.3382/ps/pev010 · 1.54 Impact Factor
  • Source
  • [Show abstract] [Hide abstract]
    ABSTRACT: Modern techniques involving molecular biology, such as metagenomics, have the advantage of exploiting a higher number of microorganisms; however, classic isolation and culture methods used to obtain antimicrobials continue to be promising, especially in the isolation of Actinobacteria, which are responsible for the production of many of these compounds. In this work, two methodologies were used to search for antimicrobial substances-isolation of Actinobacteria and metagenomics of the Atlantic Rainforest soil and of the cultivation of cocoa intercropped with acai berry in the Atlantic Rainforest. The metagenomic libraries were constructed with the CopyControl Fosmid Library kit EPICENTRE, resulting in a total of 2688 clones, 1344 of each soil sample. None of the clones presented antimicrobial activity against the microorganisms tested: S. aureus, Bacillus subtilis, and Salmonella choleraesuis. A total of 46 isolates were obtained from the isolation of soil Actinobacteria: 24 isolates from Atlantic Rainforest soil and 22 isolates from the intercrop cultivation soil. Of these, two Atlantic Rainforest soil isolates inhibited the growth of S. aureus including a clinical isolate of S. aureus MRSA-a promising result, since it is an important multidrug-resistant human pathogen.
    01/2014; 2014:1-7. DOI:10.1155/2014/909601