Impact of environmental characteristics on children's gut microbiota - A pilot study in assessing the role of indoor microbiome and metabolites

How the Built Environment Shapes Children's Microbiome: A Systematic Review

This systematic review aims to synthesize key empirical findings to understand how various elements of the built environment influence the microbiome concerning children's health and well-being. A comprehensive literature search was conducted across multiple databases, focusing on studies that examined the relationship between built environment factors and the microbiome aspects of childhood. A total of 42 studies were included in the final systematic review. We analyzed these studies from a range of different lenses, starting with basic research questions and variables to types of built environments, age groups of children, sampling strategy, bioinformatics, and the biological methods utilized. This review highlights a growing emphasis on children's exposure to nature within built environments and its potential to beneficially alter the microbiome, with 38% of studies addressing this link. It also identifies a significant research gap in connecting built environment design features (landscape and/or architectural) to microbiome outcomes and associated health, behavioral, and mental health impacts on children. The findings indicate that interventions aimed at improving the built environment quality via design could foster healthier microbiomes in children's environments. This review underscores the need for interdisciplinary research and policy initiatives that integrate microbiome science with built environment design to promote children's health and well-being.

A Sustainable Combined Approach to Control the Microbial Bioburden in the School Environment

The indoor microbiome is a dynamic ecosystem including pathogens that can impact human health. In this regard, the school environment represents the main living space of humans for many years, and an unhealthy environment can significantly condition students' health. School rooms can suffer from insufficient ventilation and the use of building materials that may favor pathogen contamination, mostly sanitized by conventional chemical-based methods, which can impact pollution, have temporary effects, and induce the selection of antimicrobial resistance (AMR) in persistent microbes. In the search for sustainable and effective methods to improve the healthiness of the classroom environment, a pre-post case-control study was performed in an Italian high school. Over a year, different interventions were sequentially placed and evaluated for their impact on bioburden and air quality, including the introduction of plants, a mechanical ventilation system, and probiotic-based sanitation (PBS) in substitution for chemical sanitation. Through continuous microbial monitoring of the enrolled school rooms, via culture-dependent and -independent methods, a remarkable bioburden level was detected at baseline (around 12,000 and 20,000 CFU/m2, before and after classes, respectively), composed mostly of Staphylococcus spp. and fungi. Some decrease in fungal contamination was observed following the introduction of plants. Still, the most significant decrease in pathogens and associated AMR was detected following the introduction of ventilation and PBS, which decreased pathogen level by >80% (p < 0.001) and AMR by up to 3 Log10 (p < 0.001) compared to controls. Collected data support the use of combined strategies to improve indoor microbial quality and confirm that PBS can effectively control bioburden and AMR spread not only in sanitary environments.

Potential effects of indoor microbiome characteristics on health: A systematic review

OBJECTIVES

This systematic review aims to assess the potential effects of exposure to microbial agents in the indoor environment on health outcomes.

STUDY DESIGN

Systematic review.

METHODS

A systematic literature search was conducted on Embase, PubMed, and Web of Science through January 2024, and reference lists of relevant articles were reviewed. Studies that investigated the relationship between indoor microbial agents and human symptoms and diseases were eligible for inclusion.

RESULTS

In total, 20 articles were considered eligible for inclusion and reported consistency and variability in the health effects of indoor microorganisms. In microbial diversity analyses, studies showed an increasing trend in microbial α-diversity in patients with allergic and inflammatory diseases and a decreasing trend in fungal α-diversity in patients with behavioral and cognitive disorders. In microbial composition analyses, phylum Cyanobacteria, genus Izhakiella, genus Rhodomicrobiu, species Aeromonas enteropelogenes, and species Brasilonema bromeliae showed a decreasing trend in allergic and inflammatory diseases, while phylum Actinomycetota, phylum Bacillota, phylum Bacteriodota, class Gammaproteobacteria and species Deinococcus gobiensis showed an increasing trend. There were fewer consistent results for respiratory infectious diseases and behavioral and cognitive disorders.

CONCLUSION

To our knowledge, this is the first systematic review of the association between indoor microbial exposure and human health risk. In this systematic review, we explored the potential impact of microbiota characterization of indoor environments on different diseases or symptoms from the perspective of microbial taxonomic levels through a comprehensive review of differential analysis of indoor microbiota diversity and composition, which provided potential intervention strategies for the management of the indoor microbiome.

MiMeJF: Application of Coupled Matrix and Tensor Factorization (CMTF) for Enhanced Microbiome-Metabolome Multi-Omic Analysis

Background/Objectives: The integration of microbiome and metabolome data could unveil profound insights into biological processes. However, widely used multi-omic data analyses often employ a stepwise mining approach, failing to harness the full potential of multi-omic datasets and leading to reduced detection accuracy. Synergistic analysis incorporating microbiome/metabolome data are essential for deeper understanding. Method: This study introduces a Coupled Matrix and Tensor Factorization (CMTF) framework for the joint analysis of microbiome and metabolome data, overcoming these limitations. Two CMTF frameworks were developed to factorize microbial taxa, functional pathways, and metabolites into latent factors, facilitating dimension reduction and biomarker identification. Validation was conducted using three diverse microbiome/metabolome datasets, including built environments and human gut samples from inflammatory bowel disease (IBD) and COVID-19 studies. Results: Our results revealed biologically meaningful biomarkers, such as Bacteroides vulgatus and acylcarnitines associated with IBD and pyroglutamic acid and p-cresol associated with COVID-19 outcomes, which provide new avenues for research. The CMTF framework consistently outperformed traditional methods in both dimension reduction and biomarker detection, offering a robust tool for uncovering biologically relevant insights. Conclusions: Despite its stringent data requirements, including the reliance on stratified microbial-based pathway abundances and taxa-level contributions, this approach provides a significant step forward in multi-omics integration and analysis, with potential applications across biomedical, environmental, and agricultural research.

An evaluation of in utero polycyclic aromatic hydrocarbon exposure on the neonatal meconium microbiome

INTRODUCTION

In utero exposure to environmental polycyclic aromatic hydrocarbon (PAH) is associated with neurodevelopmental impairments[1-8], prematurity[9-12] and low birthweight[9,13-15]. The gut microbiome serves as an intermediary between self and external environment; therefore, exploring the impact of PAH on microbiota may elucidate their role in disease. Here, we evaluated the effect of in utero PAH exposure on meconium microbiome.

METHODS

We evaluated 49 mother-child dyads within Fair Start Birth Cohort with full term delivery and adequate meconium sampling. Prenatal PAH was measured using personal active samplers worn for 48 h during third trimester. Post-processing, 35 samples with adequate biomass were evaluated for association between tertile of PAH exposure (high (H) vs low/medium (L/M)) and microbiome diversity.

RESULTS

No significant differences were observed in alpha diversity metrics, Chao1 and Shannon index, between exposure groups for total PAH. However, alpha diversity metrics were negatively associated with log benzo[a]anthracene (BaA) and log chrysene (Chry) with high exposure, but positively associated with log benzo[a]pyrene (BaP) with low/medium exposure. After adjustment for birthweight and sex, alpha diversity metrics were negatively associated with log BaA, BaP, Chry, Indeno (Zhang et al., 2021; Perera et al., 2018)pyrene (IcdP) and total PAH with high exposure. Conversely, with low/medium exposure, alpha diversity metrics positively correlated with log BaP and benzo[b]fluoranthane (BbF). No significant difference in beta diversity was observed across groups using UniFrac, weighted UniFrac, or Bray-Curtis methods. Differential expression analysis showed differentially abundant taxa between exposure groups.

CONCLUSION

Bacterial taxa were detectable in 35/49 (71%) meconium samples. Altered alpha diversity metrics and differentially abundant taxa between groups suggest in utero PAH exposure may impede early colonization. Sample size is limited, but these findings provide supporting evidence for wider scale research. Research on long-term impact of prenatal PAH exposure on childhood health outcomes is ongoing. Differential effects of specific PAHs need further evaluation.

Neuroprotective Effect of a Multistrain Probiotic Mixture in SOD1G93A Mice by Reducing SOD1 Aggregation and Targeting the Microbiota-Gut-Brain Axis

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by the selective loss of motor neurons. A bidirectional communication system known as the "microbiota-gut-brain" axis has a regulatory function in neurodegenerative disorders. The impact of probiotics on ALS through the "microbiota-gut-brain" axis remains uncertain. A longitudinal investigation was conducted to examine the alterations in the structure of the ileum and colon in mutant superoxide dismutase 1 (SOD1G93A) transgenic mice models of ALS by using immunofluorescence and Western blotting. Subsequently, the mice were administered a multistrain probiotic mixture (LBE) or vehicle orally, starting from 60 days of age until the terminal stage of the disease. The effects of these agents on the behavior, gut microbiota, microbial metabolites, and pathological processes of the spinal and intestine of SOD1G93A mice were analyzed, with a focus on exploring potential protective mechanisms. SOD1G93A mice exhibit various structural abnormalities in the intestine. Oral administration of LBE improved the proinflammatory response, reduced aberrant superoxide dismutase 1 (SOD1) aggregation, and protected neuronal cells in the intestine and spinal cord of SOD1G93A mice. Furthermore, LBE treatment resulted in a change in intestinal microbiota, an increase in short-chain fatty acid levels, and an enhancement in autophagy flux. SOD1G93A mice exhibited various structural abnormalities in the intestine. LBE can improve the proinflammatory response, reduce aberrant SOD1 aggregation, and protect neuronal cells in the spinal cord and intestine of SOD1G93A mice. The positive effect of LBE can be attributed to increased short-chain fatty acids and enhanced autophagy flux.

Butyrate attenuates cold-induced hypertension via gut microbiota and activation of brown adipose tissue

OBJECTIVE

Chronic exposure to cold temperature is known to elevate blood pressure, leading to a condition known as cold-induced hypertension (CIH). Our previous research suggested correlations between alterations in gut microbiota, decrease in butyrate level, and the onset and progression of CIH. However, the role of butyrate in CIH and the underlying mechanisms need further investigation.

METHODS

We exposed Specific Pathogen Free (SPF) rats to continuous cold temperature (4 ± 1 °C) for 6 weeks to establish a CIH rat model. Rats were divided into different groups by dose and duration, and the rats under cold were administered with butyrate (0.5 or 1 g/kg/day) daily. We assessed hypertension-associated phenotypes, pathological morphological changes, and endocrine-related phenotypes of brown adipose tissue (BAT). The effects of butyrate on gut microbiota and intestinal content metabolism were evaluated by 16s RNA sequencing and non-targeted metabolomics, respectively.

RESULTS

The systolic blood pressure (SBP) of rats exposed to cold after supplemented with butyrate were significantly lower than that of the Cold group. Butyrate may increase the species, abundance, and diversity of gut microbiota in rats. Specifically, butyrate intervention enriched beneficial bacterial genera, such as Lactobacillaceae, and decreased the levels of harmful bacteria genera, such as Actinobacteriota and Erysipeiotrichaceae. Cold exposure significantly increased BAT cells and the number of mitochondria. After butyrate supplementation, the levels of peroxisome proliferator-activated receptor gamma coactivator 1a and fibroblast growth factor 21 in BAT were significantly elevated (P < 0.05), and the volume and number of lipid droplets increased. The levels of ANG II and high-density lipoprotein were elevated in the Cold group but decreased after butyrate supplementation.

CONCLUSION

Butyrate may attenuate blood pressure in CIH by promoting the growth of beneficial bacteria and the secretion of beneficial derived factors produced by BAT, thus alleviating the elevation of blood pressure induced by cold. This study demonstrates the anti-hypertensive effects of butyrate and its potential therapeutic mechanisms, offering novel insights to the prevention and treatment of CIH in populations living or working in cold environments.

Childcare centre soil microbiomes are influenced by substrate type and surrounding vegetation condition

Urban development has profoundly reduced human exposure to biodiverse environments, which is linked to a rise in human disease. The 'biodiversity hypothesis' proposes that contact with diverse microbial communities (microbiota) benefits human health, as exposure to microbial diversity promotes immune training and regulates immune function. Soils and sandpits in urban childcare centres may provide exposure to diverse microbiota that support immunoregulation at a critical developmental stage in a child's life. However, the influence of outdoor substrate (i.e., sand vs. soil) and surrounding vegetation on these environmental microbiota in urban childcare centres remains poorly understood. Here, we used 16S rRNA amplicon sequencing to examine the variation in bacterial communities in sandpits and soils across 22 childcare centres in Adelaide, Australia, plus the impact of plant species richness and habitat condition on these bacterial communities. We show that sandpits had distinct bacterial communities and lower alpha diversity than soils. In addition, we found that plant species richness in the centres' yards and habitat condition surrounding the centres influenced the bacterial communities in soils but not sandpits. These results demonstrate that the diversity and composition of childcare centre sandpit and soil bacterial communities are shaped by substrate type, and that the soils are also shaped by the vegetation within and surrounding the centres. Accordingly, there is potential to modulate the exposure of children to health-associated bacterial communities by managing substrates and vegetation in and around childcare centres.