Biology subjects

Salonen, A.

Publications and source records attributed to Salonen, A..

6 recordsLinked to original sources

bioRxiv2025

Infant gut microbiota in multi-child families converges with adults without a sibling-specific signature

The human gut microbiota undergoes rapid development during early life. Sibling presence has been associated with altered infant microbiota composition and accelerated maturation, but distinguishing direct microbial transmission between siblings from confounding by maternal reproductive history (parity) remains challenging. We analysed >5,000 faecal samples from >800 mother-father-infant triads in the Finnish HELMi birth cohort to characterise microbiota patterns that could inform underlying mechanisms. While sibling presence was associated with accelerated microbiota maturation and modest compositional differences, infants who both had siblings (or both lacked siblings) were no more similar to each other than mixed pairs. Instead, infants with siblings exhibited non-specific convergence with adult microbiota profiles and contributed fewer unique genera to their family metacommunities (infant-mother-father triads). Multi-child families harboured smaller but compositionally distinct metacommunities. These patterns challenge simple models of direct sibling transmission and suggest that multiple factors associated with family structure may jointly influence infant microbiota development, though specific mechanisms remain unclear.

microbiology↗

bioRxiv2025

Low-dimensional brain-symptom associations delineate depression phenotypes with distinct connectivity biomarkers and symptom profiles

Depression is neurobiologically and clinically heterogeneous. New approaches using resting-state functional MRI (rs-fMRI) functional connectivity (FC) data have modeled the neural basis of depression heterogeneity and revealed unique neural phenotypes. Yet, no studies have identified depression phenotypes from electrophysiological magnetoencephalography (MEG) data although MEG measures human brain dynamics at millisecond precision. We demonstrate here unique depression phenotypes based on MEG-oscillation FC. We collected resting-state MEG, MRI, and clinical symptom data from 263 patients with unipolar depression and 75 healthy controls. We assessed MEG-FC with two oscillatory coupling-mode measures that are fundamental for information processing. To define normative phenotypes, we computed their latent-space low-dimensional brain-symptom associations, and used these components to identify phenotypes using unsupervised machine learning. We identified five stable depression phenotypes that were characterized by unique symptom profiles and distinct spectral patterns. Our results demonstrate new neural underpinnings of depression heterogeneity and reveal unique neural phenotypes with potential personalized diagnostic value.

neuroscience↗

bioRxiv2025

Associations between infant gut microbiota and the living environment

The human gut microbiota is central to health and development of the host, and early life microbiota is affected by a range of factors that can alter the infants development for years to come. The role of the external, natural environment in shaping the gut microbiota is still largely unknown. We examined how the environment surrounding the home, in terms of land use, air quality, biodiversity, and traffic and road characteristics associate with the infant gut microbiota in the first two years of life with data from 893 children from the longitudinal birth cohort HELMi. We show that the environment has a minimal overall association with the microbiota development. Air quality explained the largest degree of variation in microbiota composition, while proximity to agriculture appeared to have a similar effect as poor air quality during the first 6 months, while open grey space and agriculture had similar associations after 6 months. The results suggest that the infant gut microbiota is not strongly dependent on the external natural environment, and that the impact of the environment is mostly mediated by exposure to pollution that may affect the hosts immune system and indirectly the gut microbiota.

microbiology↗

bioRxiv2024

The Aggregated Gut Viral Catalogue (AVrC): A Unified Resource for Exploring the Viral Diversity of the Human Gut

Despite the growing interest in the role of the gut virome in human health and disease, identifying viral sequences from human gut metagenomes remains computationally challenging due to underrepresentation of viral genomes in reference databases. Several recent large-scale efforts have mined human gut metagenomes to establish viral sequence catalogues, using varied computational tools and quality control criteria. However, there has been no consistent comparison of these catalogues quality, diversity, and completeness, nor unification into a comprehensive resource. Here, we systematically surveyed nine previously published human gut viral catalogues, assessing their quality and the overlap of the viral sequences retrieved. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy. We further expanded representation by mining 7,867 infant gut metagenomes, retrieving 1,205,739 additional putative viral sequences. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Detailed annotations were generated for sequence quality, taxonomy, predicted lifestyle, and putative host. The AVrC reveals the gut viromes substantial unexplored diversity, providing a pivotal resource for viral discovery. The AVrC is accessible as a relational database and through a web interface allowing customized querying and subset retrieval, enabling streamlined utilization by the research community and future expansions as novel data becomes available. Author summaryThe human gut is home to a vast array of viruses, collectively known as the gut virome, which play a crucial role in human health and disease. Recently, several research groups aiming at providing an overview of the Human gut viral diversity, have created catalogues of viral sequences found in the human gut by analyzing a large number of fecal samples from different individuals. In this study, we compared nine of these existing catalogues and found that there was surprisingly little overlap between them, with 82% of the viral sequences being unique to a single catalogue. To further expand the available data, we analyzed nearly 8,000 additional fecal samples from infants. By combining all this ressources, we created a unified resource called the Aggregated Gut Viral Catalogue (AVrC), which contains more than a million distinct viral sequences, representing nearly 450,000 different viral species. This catalogue, which is easily accessible to the scientific community through a user-friendly web interface, provides a valuable tool for exploring the vast diversity of the human gut virome and its potential implications for human health.

microbiology↗

bioRxiv2022

Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus

Biogeographic variations in the gut microbiota reflect host and environmental factors delineating human populations, and are pivotal to understand global patterns of host-microbiota interactions in health and prevalent lifestyle-related diseases, such as type 2 diabetes mellitus (T2D). Pakistani adults, having an exceptionally high prevalence of T2D, are one of the most understudied populations in microbiota research to date. The aim of the present study is to examine the gut microbiota across individuals from Pakistan and other populations of non-industrialized and industrialized lifestyles with a focus on T2D. The fecal samples from 94 urban-dwelling Pakistani adults with and without T2D were profiled by 16S ribosomal RNA gene amplicon sequencing and qPCR, and plasma samples quantified for circulating levels of lipopolysaccharide binding protein (LBP) and the activation ability of Toll-like receptor (TLR)-signaling. Publicly available datasets generated with comparable molecular methods were retrieved for comparative analysis. Overall, urbanized Pakistanis gut microbiota was similar to that of transitional or non-industrialized populations, depleted in Akkermansiaceae and enriched in Prevotellaceae (dominated by the non-Westernized clades of Prevotella copri). The relatively high proportion of Atopobiaceae appeared to be a unique characteristic of the Pakistani gut microbiota. The Pakistanis with T2D had elevated levels of LBP and TLR-signaling in circulation as well as gut microbial signatures atypical of other populations e.g., increased relative abundance of Libanicoccus/Parolsenella, limiting the inter-population extrapolation of gut microbiota-based classifiers for T2D. Taken together, our findings call for more global representation of understudied populations to extend the applicability of microbiota-based diagnostics and therapeutics.

microbiology↗

bioRxiv2018

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling

The use of relative next generation sequencing (NGS) abundance data can lead to misinterpretations of microbial community structures as the increase of one taxon leads to concurrent decrease of the other(s). To overcome compositionality, we provide a quantitative NGS solution, which is achieved by adjusting the relative 16S rRNA gene amplicon NGS data with quantitative PCR (qPCR-based) total bacterial counts. By comparing the enumeration of dominant bacterial groups on different taxonomic levels in human fecal samples using taxon-specific 16S rRNA gene-targeted qPCR we show that quantitative NGS is able to estimate absolute bacterial abundances accurately. We also observed a higher degree of correspondence in the estimated microbe-metabolite relationship when quantitative NGS was applied. Being conceptually and methodologically analogous to amplicon-based NGS, our qPCR-based method can be readily incorporated into the standard, high-throughput NGS sample processing pipeline for more accurate description of interactions within and between the microbes and host.

microbiology↗