Association of indoor dust microbiota with cognitive function and behavior in preschool-aged children

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.

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.

Associations of indoor airborne microbiome with lung function: evidence from a randomized, double-blind, crossover study of microbial intervention

Microorganisms constitute an essential component of the indoor ecosystem and may pose potential health risks after inhalation. However, evidence regarding the impact of indoor airborne microbiome on general respiratory health is scarce. Additionally, while air purification has been shown to be an effective strategy for controlling culturable bioaerosols, its impact on indoor airborne microbiome remains unclear. To determine the impact of indoor airborne microbial exposure on lung function, and whether and how air purification can modify indoor airborne microbiome, we conducted a randomized, double-blind, crossover study employing air purification intervention among 68 healthy young adults in Beijing, China. Indoor airborne bacteria and fungi were characterized using amplicon sequencing technology and quantified by qPCR. Our results indicated positive associations between indoor airborne microbial α-diversity and lung function indices; however, adverse effects from total microbial load were observed. Males were more susceptible to microbial exposure than females. Beneficial effects from richness in Actinobacteria, Bacteroidia, Oxyphotobacteria, Bacilli, Clostridia, Alphaproteobacteria, Gammaproteobacteria, Dothideomycetes, and Sordariomycetes, and detrimental effects from five Proteobacteria genera, including Dechloromonas, Hydrogenophaga, Klebsiella, Pseudomonas, and Tolumonas, were also identified. Air purification contributed to decreased fungal diversity and total fungal load, but not the overall microbial community structure. Our study demonstrates the significant role of indoor airborne microbiome in regulating human respiratory health and provides inspiration for improving health through manipulation of indoor microbiome. Meanwhile, our study also underscores the importance of balancing the potential benefits from decreased microbial load and the underlying risks from reduced microbial diversity while applying environmental microbial interventions.

Does gut microbiota dysbiosis impact the metabolic alterations of hydrogen sulfide and lanthionine in patients with chronic kidney disease?

BACKGROUND

Chronic Kidney Disease (CKD) is characterized by a methionine-related metabolic disorder involving reduced plasma levels of hydrogen sulfide (H2S) and increased lanthionine. The gut microbiota influences methionine metabolism, potentially impacting sulfur metabolite dysfunctions in CKD. We evaluated whether gut microbiota dysbiosis contributes to H2S and lanthionine metabolic alterations in CKD.

METHODS

The gut microbiota of 88 CKD patients (non-dialysis, hemodialysis, and transplant patients) and 26 healthy controls were profiled using 16 S-amplicon sequencing. H2S and lanthionine concentrations were measured in serum and fecal samples using the methylene blue method and LC-MS/MS, respectively.

RESULTS

The CKD population exhibited a tenfold increase in serum lanthionine associated with kidney dysfunction. Despite lanthionine retention, hemodialysis and transplant patients had significantly lower serum H2S than healthy controls. Fecal H2S levels were not altered or related to bloodstream H2S concentrations. Conversely, fecal lanthionine was significantly increased in CKD compared to healthy controls and associated with kidney dysfunction. Microbiota composition varied among CKD groups and healthy controls, with the greatest dissimilarity observed between hemodialysis and transplant patients. Changes relative to the healthy group included uneven Ruminococcus gnavus distribution (higher in transplant patients and lower in non-dialysis CKD patients), reduced abundance of the short-chain fatty acid-producing bacteria Alistipes indistinctus and Coprococcus eutactus among transplant patients, and depleted Streptococcus salivarius in non-dialysis CKD patients. A higher abundance of Methanobrevibacter smithii, Christensenella minuta, and Negativibacillus massiliensis differentiated hemodialysis patients from controls. No correlation was found between differentially abundant species and the metabolic profile that could account for the H2S and lanthionine alterations observed.

CONCLUSIONS

The metabolic deregulation of H2S and lanthionine observed in the study was not associated with alterations in the gut microbiota composition in CKD patients. Further research on microbial sulfur pathways may provide a better understanding of the role of gut microbiota in maintaining H2S and lanthionine homeostasis.

Height-Resolved Analysis of Indoor Airborne Microbiome: Comparison with Floor Dust-Borne Microbiome and the Significance of Shoe Sole Dust

Exposure to the indoor airborne microbiome is closely related to the air that individuals breathe. However, the floor dust-borne microbiome is commonly used as a proxy for indoor airborne microbiome, and the spatial distribution of indoor airborne microbiome is less well understood. This study aimed to characterize indoor airborne microorganisms at varying heights and compare them with those in floor dust. An assembly of three horizontally and three vertically positioned Petri dishes coated with mineral oil was applied for passive air sampling continuously at three heights without interruption. The airborne microbiomes at the three different heights showed slight stratification and differed significantly from those found in the floor dust. Based on the apportionment results from the fast expectation-maximization algorithm (FEAST), shoe sole dust contributed approximately 4% to indoor airborne bacteria and 14% to airborne fungi, a contribution that is comparable to that from the floor dust-borne microbiome. The results indicated that floor dust may not be a reliable proxy for indoor airborne microbiome. Moreover, the study highlights the need for height-resolved studies of indoor airborne microbiomes among humans in different activity modes and life states. Additionally, shoe sole-dust-associated microorganisms could potentially be a source to "re-wild" the indoor microbiota.

Comparative Metagenomic Analysis of Seed Endobiome of Domesticated and Wild Finger Millet Species (Eleusine spp.): Unveiling Microbial Diversity and Composition

Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.

Unveiling the overlooked microbial niches thriving on building exteriors

Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.

A novel birnavirus identified as the causative agent of summer atrophy of pearl oyster (Pinctada fucata (Gould))

The Akoya pearl oyster (Pinctada fucata (Gould)) is the most important species for pearl cultivation in Japan. Mass mortality of 0-year-old juvenile oysters and anomalies in adults, known as summer atrophy, have been observed in major pearl farming areas during the season when seawater temperatures exceed about 20 °C since 2019. In this study, we identified a novel birnavirus as the pathogen of summer atrophy and named it Pinctada birnavirus (PiBV). PiBV was first presumed to be the causative agent when it was detected specifically and frequently in the infected oysters in a comparative metatranscriptomics of experimentally infected and healthy pearl oysters. Subsequently, the symptoms of summer atrophy were reproduced by infection tests using purified PiBV. Infection of juvenile oysters with PiBV resulted in an increase in the PiBV genome followed by the atrophy of soft body and subsequent mortality. Immunostaining with a mouse antiserum against a recombinant PiBV protein showed that the virus antigen was localized mainly in the epithelial cells on the outer surface of the mantle. Although the phylogenetic analysis using maximum likelihood method placed PiBV at the root of the genus Entomobirnavirus, the identity of the bi-segmented, genomic RNA to that of known birnaviruses at the full-length amino acid level was low, suggesting that PiBV forms a new genus. The discovery of PiBV will be the basis for research to control this emerging disease.

What evidence exists regarding the impact of biodiversity on human health and well-being? A systematic map protocol

BACKGROUND

Global biodiversity is rapidly declining, yet we still do not fully understand the relationships between biodiversity and human health and well-being. As debated, the loss of biodiversity or reduced contact with natural biodiversity may lead to more public health problems, such as an increase in chronic disease. There is a growing body of research that investigates how multiple forms of biodiversity are associated with an increasingly diverse set of human health and well-being outcomes across scales. This protocol describes the intended method to systematically mapping the evidence on the associations between biodiversity from microscopic to planetary scales and human health and well-being from individual to global scales.

METHODS

We will systematically map secondary studies on the topic by following the Collaborations for Environmental Evidence Guidelines and Standards for Evidence Synthesis in Environment Management. We developed the searching strings to target both well established and rarely studied forms of biodiversity and human health and well-being outcomes in the literature. A pairwise combination search of biodiversity and human health subtopics will be conducted in PubMed, Web of Science platform (across four databases) and Scopus with no time restrictions. To improve the screening efficiency in EPPI reviewer, supervised machine learning, such as a bespoke classification model, will be trained and applied at title and abstract screening stage. A consistency check between at least two independent reviewers will be conducted during screening (both title-abstract and full-text) and data extraction process. No critical appraisal will be undertaken in this map. We may use topic modelling (unsupervised machine learning) to cluster the topics as a basis for further statistical and narrative analysis.

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat

BACKGROUND

The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses.

RESULTS

Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum).

CONCLUSIONS

Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.

Th17-associated cytokines IL-17 and IL-23 in inflamed skin of Darier disease patients as potential therapeutic targets

Darier disease (DD) is a rare, inherited multi-organ disorder associated with mutations in the ATP2A2 gene. DD patients often have skin involvement characterized by malodorous, inflamed skin and recurrent, severe infections. Therapeutic options are limited and inadequate for the long-term management of this chronic disease. The aim of this study was to characterize the cutaneous immune infiltrate in DD skin lesions in detail and to identify new therapeutic targets. Using gene and protein expression profiling assays including scRNA sequencing, we demonstrate enhanced expression of Th17-related genes and cytokines and increased numbers of Th17 cells in six DD patients. We provide evidence that targeting the IL-17/IL-23 axis in a case series of three DD patients with monoclonal antibodies is efficacious with significant clinical improvement. As DD is a chronic, relapsing disease, our findings might pave the way toward additional options for the long-term management of skin inflammation in patients with DD.

Deciphering the distribution of microbial communities and potential pathogens in the household dust

The reliance of modern society on indoor environments increasing has made them crucial sites for human exposure to microbes. Extensive research has identified ecological drivers that influence indoor microbial assemblages. However, few studies have examined the dispersion of microbes in different locations of identical indoor environments. In this study, we employed PacBio Sequel full-length amplicon sequencing to examine the distribution of microbes at distinct locations in a single home and to identify the potential pathogens and microbial functions. Microbial communities differed considerably among the indoor sampling sites (P < 0.05). In addition, bacterial diversity was influenced by human activities and contact with the external environment at different sites, whereas fungal diversity did not significantly differ among the sites. Potential pathogens, including bacteria and fungi, were significantly enriched on the door handle (P < 0.05), suggesting that door handles may be hotpots for potential pathogens in the household. A high proportion of fungal allergens (34.37 %-56.50 %), which can cause skin diseases and asthma, were observed. Co-occurrence network analysis revealed the essential ecological role of microbial interactions in the development of a healthy immune system. Overall, we revealed the differences in microbial communities at different sampling sites within a single indoor environment, highlighting the distribution of potential pathogens and ecological functions of microbes, and providing a new perspective and information for assessing indoor health from a microbiological viewpoint.