How indoor environment impacts the microbiota balance

The human gut harbors millions of microbes, primarily bacteria, which have positive and adverse health effects. A recent Environmental Research journal paper evaluated how indoor microbiomes and metabolites affect the human gut microbiota.

Study: Impact of environmental characteristics on childrenStudy: Impact of environmental characteristics on children’s gut microbiota – A pilot study in assessing the role of indoor microbiome and metabolites. Image Credit: CI Photos / Shutterstock


Gut bacterial dysbiosis has been associated with the incidence of many diseases, such as colorectal cancer, inflammatory skin diseases, and chronic kidney disease. Several indexes, such as the Shannon index, Simpson index, Gut Microbiome Health Index (GMHI), and Faith’s PD, have been developed to examine gut health by measuring microbial diversity and abundance.

Several studies have indicated that the surrounding environment and an individual’s lifestyle significantly influence gut microbiota. Interestingly, it has been noted that children exposed to pets have an altered abundance of gut microbiota taxa, and those exposed to house dust and soil have shown elevated gut microbial diversity. Persons residing near green areas have enhanced α-diversity of the human gut. In contrast, those living in areas with high levels of air pollution are at a high risk of gut microbial dysbiosis, which impacts metabolic health.

Previous studies have indicated an association between indoor microbiome and microbial metabolites with chronic diseases (e.g., rhinitis, asthma, sick-building syndrome, and dermatitis). Common indoor microbiota, such as Collinsella, Aspergillus subversicolor, and Cutibacterium have been linked with the incidence of many chronic diseases. However, not all indoor microbes have negative effects. For instance, the presence of Lactobacillus iners, Prevotella and Dolosigranulum in the indoor environment is negatively associated with the incidence of rhinitis. In addition, some indoor microbiome (e.g., Clostridium difficile) also modulates human gut microbiota.

Diet plays a crucial role in gut microbial population and abundance. A diet rich in fiber favors beneficial bacteria, while a high-fat diet enhances the level of harmful bacteria, which promotes gut inflammation and alters intestinal permeability. More research is required to comprehend the impact of indoor microbiomes and metabolites on gut microbiota composition and diversity.

About the Study

This pilot study assessed the impact of indoor microbiome and metabolites on the human gut microbiota. A total of 56 children between the age of 3 and 10, were recruited in this study. Electronic questionnaires were used to collect health information and relevant environmental characteristics. A distance-weighted method was used to estimate the annual outdoor air pollutants.

Fecal samples were obtained from the participants, and dust samples were collected using a sterile sampler. DNA was extracted from the dust samples and was analyzed using a culture-independent shotgun metagenomic sequencing technique. In addition, liquid chromatography-mass spectrometry (LC-MS) was used for the chemical profiling of the dust samples.

The associations between environmental microbial and non-microbial characteristics and the diversity/composition of the gut microbiota were investigated using PERMANOVA and regression models. In addition, the effect of environmental characteristics on GMHI was also examined.

Study Findings

The children recruited in this study were randomly selected from twelve out of sixteen districts in Shanghai, China. The study cohort consisted of 38% boys and 62% girls. More than half of the cohort had siblings, and around 59% of children had pets or indoor plants during their early childhood. Twenty-one children resided in an area of heavy traffic. Some children had started kindergarten. Around 16% of children were exposed to environmental tobacco smoking during their early childhood. 

A total of 6,247 microbes were characterized from the indoor dust samples. The majority of microbes belonged to classes Bacilli, Gammaproteobacteria, and Actinobacteria, followed by Bacteroidia, Flavobacteria, Alphaproteobacteria, Betaproteobacteria, Clostridia, and Tissierellia. Some of the most abundantly found microbial species are Cutibacterium acnesStaphylococcus aureusStaphylococcus epidermidis, and Micrococcus luteus

Facultative pathogens, such as Pseudomonas aeruginosaMycobacterium tuberculosis, and Klebsiella pneumoniae, were also detected. Virulence factors (VFs) and antimicrobial resistance genes (ARGs) were determined using molecular sequencing techniques. VFs were predominantly derived from facultative pathogens.

A total of 1,442 metabolites and chemicals were characterized via the second stage of mass spectrometry (MS2). Metabolites, such as primarily lipids (e.g., fatty acyl, flavonoid, and steroid derivatives), xenobiotics, amino acids, carbohydrates, cofactors, and vitamins, were identified during chemical profiling.

A total of 318 bacteria were characterized from gut samples that belong to phyla Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Children’s gut was enriched with Flavonifractor plautii, Oscillibacter, and Faecalibacterium. The age of children and the time when they started kindergarten had a significant impact on gut microbial composition. In addition, residing near heavy traffic also influenced gut microbial composition.

Among dietary characteristics, the frequency of drinking soft drinks substantially impacted gut microbial composition. The abundance of indoor metabolites and chemicals did not have any impact on the overall gut microbial composition.


The authors claim this study to be the first to examine the association between indoor microbiome/metabolites and gut microbiota. This study highlighted how indoor microbe exposure influences the human gut microbiota.

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