Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions

Abstract

Microorganisms are widely distributed all over the Earth, inhabiting very diverse natural ecosystems, from the human body to inanimate indoor environments. Until recently, the methods most commonly used to study microbes have been culture-dependent approaches relying on the phenotypic evaluation of isolates that can grow in laboratory conditions. Given the advances in molecular biology and high-throughput DNA sequencing methodologies, scientists could expand their microbiome knowledge to microorganisms that do not grow well in the laboratory or have been considered too difficult and laborious to be cultivated. Culture-independent methods such as direct DNA sequencing can be performed for many samples at once, revealing the entire microbial profile of the samples and making possible the rapid characterization of the whole environmental microbiome. Investigating the microbiome profile of indoor environments such as hospitals, houses, offices and other buildings is of major concern because it could include a number of opportunistic, pathogenic or nosocomial microbes. Additionally, these environments could serve as reservoirs of virulence or antimicrobial resistance, which could be spread by humans or other vectors. High-throughput DNA sequencing has enabled large-scale microbiome screening for multiple indoor areas in a single analysis. Using this approach, we can easily track microorganisms in the environment and monitor microbiome composition related to hygiene processes or environment quality. Gaining such information and resolution regarding indoor microbiome analysis can lend very important assistance for epidemiological surveillance. Impact statement Research concerning the microbiome of indoor environments like hospitals, houses or buildings could have several implications for human health. Today, there is an ongoing shift in the paradigm of microbial analysis, from single isolated bacterial samples to entire microbiome profiles using high-throughput DNA sequencing methods. The use of sequencing methods in several studies has revealed an unprecedented microbial diversity in indoor environments, leading to a larger comprehension of the entire microbiome context. Here, we present a review of these microbiome studies using high-throughput DNA sequencing, including some new approaches and ideas that can be broadly applied in microbial tracking and epidemiological surveillance of indoor environments.

Cytokines Levels and Salivary Microbiome Play A Potential Role in Oral Lichen Planus Diagnosis

“…The data presented in this manuscript was generated by Neoprospecta Microbiome Technologies as previously described 23,24 . Briefly, microbial DNA from four (2 OLP and 2 NSIL) saliva pellet samples was obtained using AMPureXP beads (Beckman Coulter, Brea, CA) after a thermal lysis process of 96 °C for 10 min.…”

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces

“…This extensive investigations became possible due to the dissemination of culture-independent microbiology methods using next-generation DNA sequencing directly from the collected samples. Culture-independent methods like DNA sequencing, are less time-consuming and less skewed to detect only specific cultivable microorganisms compared to traditional microbiological methods, allowing large-scale screening of microorganisms, including those that will not grow well in conventional microbiology conditions [5][6][7][8][9].…”

The Catenulida flatworm can express genes from its microbiome or from the DNA it ingests

“…The microbiome analysis was performed by Neoprospecta (https://neoprospecta.com). Regions of the 16S ribosomal gene were amplified by PCR and sequenced with an Illumina platform, as described previously 38,39 . The primers and PCR conditions used are available in Supplementary Table 3.…”