Comparative analysis of impact of human occupancy on indoor microbiomes

Linkage of in-refrigerator water dispensing systems to elevated exposure to microbial contamination at the microbiome scale

In-refrigerator water dispensing systems are ubiquitous in residential homes with tap water as the inflow. Passage through these systems resulted in significant microbial growth in the water, with the abundance of potential opportunistic pathogens Mycobacterium and Pseudomonas increasing by 8,053- and 221-fold, respectively. Elevated exposure to microbial contaminants linked to in-refrigerator water dispensing systems may represent a significant public health concern.

Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas

Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.

Alternating polarity as a novel strategy for building synthetic microbial communities capable of robust Electro-Methanogenesis

Electro-methanogenic microbial communities can produce biogas with high efficiency and have attracted extensive research interest. In this study an alternating polarity strategy was developed to build electro-methanogenic communities. In two-chamber bioelectrochemical systems amended with activated carbon, the electrode potential was alternated between +0.8 V and -0.4 V vs. standard hydrogen electrode every three days. Cumulative biogas production under alternating polarity increased from 45 L/L/kg-activated carbon after start-up to 125 L/L/kg after the 4th enrichment, significantly higher than that under intermittent cathode (-0.4 V/open circuit), continuous cathode (-0.4 V), and open circuit. The communities assembled under alternating polarity were electroactive and structurally different from those assembled under other conditions. One Methanobacterium population and two Geobacter populations were consistently abundant and active in the communities. Their 16S rRNA was up-regulated by electrode potentials. Bayesian networks inferred close associations between these populations. Overall, electro-methanogenic communities have been successfully assembled with alternating polarity.

Distribution characteristics and potential risks of bioaerosols during scattered farming

In most economically underdeveloped areas, scattered farming and human‒livestock cohabitation are common. However, production of bioaerosols and their potential harm in these areas have not been previously researched. In this study, bioaerosol characteristics were analyzed in scattered farming areas in rural Northwest China. The highest bacteria, fungi, and Enterobacteria concentrations were 125609 ± 467 CFU/m³, 25175 ± 10305 CFU/m³, and 4167 ± 592 CFU/m³, respectively. Most bioaerosols had particle sizes >3.3 μm. A total of 71 bacterial genera and 16 fungal genera of potential pathogens were identified, including zoonotic potential pathogenic genera. Moreover, our findings showed that the scattered farming pattern of human‒animal cohabitation can affect the indoor air environment in the surrounding area, leading to chronic respiratory diseases in the occupants. Therefore, relevant government departments and farmers should enhance their awareness of bioaerosol risks and consider measures that may be taken to reduce them.

Microbes within the building envelope-a case study on the patterns of colonization and potential sampling bias

Humans are exposed to diverse communities of microbes every day. With more time spent indoors by humans, investigations into the communities of microbes inhabiting occupied spaces have become important to deduce the impacts of these microbes on human health and building health. Studies so far have given considerable insight into the communities of the indoor microbiota humans interact with, but mainly focus on sampling surfaces or indoor dust from filters. Beneath the surfaces though, building envelopes have the potential to contain environments that would support the growth of microbial communities. But due to design choices and distance from ground moisture, for example, the temperature and humidity across a building will vary and cause environmental gradients. These microenvironments could then influence the composition of the microbial communities within the walls. Here we present a case study designed to quantify any patterns in the compositions of fungal and bacterial communities existing in a building envelope and determine some of the key variables, such as cardinal direction, distance from floor or distance from wall joinings, that may influence any microbial community composition variation. By drilling small holes across walls of a house, we extracted microbes onto air filters and conducted amplicon sequencing. We found sampling height (distance from the floor) and cardinal direction the wall was facing caused differences in the diversity of the microbial communities, showing that patterns in the microbial composition will be dependent on sampling location within the building. By sampling beneath the surfaces, our approach provides a more complete picture of the microbial condition of a building environment, with the significant variation in community composition demonstrating a potential sampling bias if multiple sampling locations across a building are not considered. By identifying features of the built environment that promote/retard microbial growth, improvements to building designs can be made to achieve overall healthier occupied spaces.

Microbiome-scale analysis of aerosol facemask contamination during nebulization therapy in hospital

BACKGROUND

Microbial contamination of aerosol facemasks could be a source of nosocomial infections during nebulization therapy in hospital, prompting efforts to identify these contaminants. Identification of micro-organisms in medical devices has traditionally relied on culture-dependent methods, which are incapable of detecting the majority of these microbial contaminants. This challenge could be overcome with culture-independent sequencing-based techniques that are suited for the profiling of complex microbiomes.

AIM

To characterize the microbial contaminants in aerosol facemasks used for nebulization therapy, and identify factors influencing the composition of these microbial contaminants with the acquisition and analysis of comprehensive microbiome-scale profiles using culture-independent high-throughput sequencing.

METHODS

Used aerosol facemasks collected from hospitalized patients were analysed with culture-independent 16S rRNA gene-based amplicon sequencing to acquire microbiome-scale comprehensive profiles of the microbial contaminants. Microbiome-based analysis was performed to identify potential sources of microbial contamination in facemasks.

FINDINGS

Culture-independent high-throughput sequencing was demonstrated for the capacity to acquire microbiome-scale profiles of microbial contaminants on aerosol facemasks. Microbial source identification enabled by the microbiome-scale profiles linked microbial contamination on aerosol facemasks to the human skin and oral microbiota. Antibiotic treatment with levofloxacin was found to reduce contamination of the facemasks by oral microbiota.

CONCLUSION

Sequencing-based microbiome-scale analysis is capable of providing comprehensive characterization of microbial contamination in aerosol facemasks. Insight gained from microbiome-scale analysis facilitates the development of effective strategies for the prevention and mitigation of the risk of nosocomial infections arising from exposure to microbial contamination of aerosol facemasks, such as targeted elimination of potential sources of contamination.

Determinants of bacterial and fungal microbiota in Finnish home dust: Impact of environmental biodiversity, pets, and occupants

The indoors is where many humans spend most of their time, and are strongly exposed to indoor microbiota, which may have multifaceted effects on health. Therefore, a comprehensive understanding of the determinants of indoor microbiota is necessary. We collected dust samples from 295 homes of families with young children in the Helsinki region of Finland and analyzed the bacterial and fungal composition based on the 16S rRNA and ITS DNA sequences. Microbial profiles were combined with extensive survey data on family structure, daily life, and physical characteristics of the home, as well as additional external environmental information, such as land use, and vegetational biodiversity near the home. Using permutational multivariate analysis of variance we explained 18% of the variation of the relative abundance between samples within bacterial composition, and 17% of the fungal composition with the explanatory variables. The fungal community was dominated by the phyla Basidiomycota, and Ascomycota; the bacterial phyla Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria were dominant. The presence of dogs, multiple children, and firewood were significantly associated with both the fungal and bacterial composition. Additionally, fungal communities were associated with land use, biodiversity in the area, and the type of building, while bacterial communities were associated with the human inhabitants and cleaning practices. A distinction emerged between members of Ascomycota and Basidiomycota, Ascomycota being more abundant in homes with greater surrounding natural environment, and potential contact with the environment. The results suggest that the fungal composition is strongly dependent on the transport of outdoor environmental fungi into homes, while bacteria are largely derived from the inhabitants.

Microbiome Profiles of Nebulizers in Hospital Use

Background: Nebulizers are used to provide treatment to respiratory patients. Concerns over nosocomial infection risks from contaminated nebulizers raise the critical need to identify all microbial populations in nebulizers used by patients. However, conventional culture-dependent techniques are inadequate with the ability to identify specific microbial populations only. Therefore, the aims of this study were to acquire complete profiles of microbiomes in nebulizers used by in-patients with culture-independent high-throughput sequencing and identify sources of microbial contaminants for the development of effective practices to reduce microbial contamination in nebulizer devices. Methods: This study was conducted at the University of Tennessee Medical Center in Knoxville, TN. Nebulizers were collected between May 2018 and October 2018 from inpatients admitted to the floors for pneumonia or chronic obstructive pulmonary disease exacerbations. Nebulizers were sampled for 16S rRNA gene-based amplicon sequencing to profile nebulizer microbiomes and perform phylogenetic analysis. A Bayesian community-wide culture-independent microbial source tracking technique was used to quantify the contribution of human-associated microbiota as potential sources of nebulizer contamination. Results: Culture-independent sequencing detected diverse microbial populations in nebulizers, represented by 18 abundant genera. Stenotrophomonas was identified as the most abundant genus, accounting for 12.4% of the nebulizer microbiome, followed by Rhizobium, Staphylococcus, Streptococcus, and Ralstonia. Phylogenetic analysis revealed the presence of multiple phylotypes with close relationship to potential pathogens. Contributing up to 15% to nebulizer microbiomes, human-associated microbiota was not identified as the primary sources of nebulizer contamination. Conclusion: Culture-independent sequencing was demonstrated to be capable of acquiring comprehensive profiles of microbiomes in nebulizers used by in-patients. Phylogenetic analysis identified differences in pathogenicity between closely related phylotypes. Microbiome profile-enabled community-wide culture-independent microbial source tracking suggested greater importance of environmental sources than human sources as contributors to nebulizer microbiomes, providing important insight for the development of effective strategies for the monitoring and control of nebulizer devices to mitigate infection risks in the hospital.

Impact of building closures during the COVID-19 pandemic on Legionella infection risks

Prolonged building closures are prevalent during the COVID-19 pandemic, resulting in extreme stagnation in building water systems. High-throughput sequencing analysis revealed significantly increased presence of Legionella due to extreme water stagnation, highlighting elevated exposure risks to Legionella from building water systems during re-opening of previously closed buildings.

The Impacts of the Occupants on the Bacterial Communities of Classrooms

In modern societies, people spend most of their time in the built environment which harbors unique microbial assemblages with the potential to influence human health. However, how the occupants of buildings influence indoor microbial communities remains under-researched. Here, we investigated the diversities of the bacterial communities of a typical Chinese middle school to demonstrate the effects of occupant activities on bacterial communities inside classrooms. The results showed that samples taken from classrooms exhibited higher microbial diversity compared to samples collected from public areas such as gym and restaurant, suggesting the occupant activities could increase the diversities of the indoor microbial communities. Moreover, we also found that the duration of occupation strongly influence the presence/absence of phylogenetic lineages of the bacterial communities, the type of occupants, on the other hand, affect the relative abundances of bacterial taxa. In addition, samples taken from classrooms with longer occupation time exhibited a better fit to the Sloan Neutral Community Model for Prokaryotes, suggesting that room occupation influences the assembly process of microbial communities. In conclusion, our study demonstrates that the duration of occupation and the type of occupants influence the microbiome of the built environment.