Leo Lahti

University of Turku | UTU · Department of Mathematics and Statistics

\textbf{Motivation:}$ Hierarchical data structures are prevalent across several fields of research, as they represent an organised and efficient approach to study complex interconnected systems. Their significance is particularly evident in microbiome analysis, where microbial communities are classified at various taxonomic levels along the phyloge...

Background/objectives: Obesity impairs intestinal glucose uptake (GU) (intestinal uptake of circulating glucose from blood) and alters gut microbiome. Exercise improves intestinal insulin-stimulated GU and alters microbiome. Genetics influence the risk of obesity and gut microbiome. However, the role of genetics on the effects of exercise on intes...

This research presents an advanced fractional-order compartmental model designed to delve into the complexities of COVID-19 transmission dynamics, specifically accounting for the influence of environmental pathogens on disease spread. By enhancing the classical compartmental framework, our model distinctively incorporates the effects of order deriv...

The gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort ( n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composit...

The spread of antibiotic-resistance genes in bacteria has severely reduced the efficacy of antibiotics, now contributing to 1.3 million deaths annually. Despite the far-reaching epidemiological implications of this trend, the extent to which antimicrobial resistance load varies within human populations and the drivers that contribute most to this v...

Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the H...

We introduce FdeSolver, an open-source Julia package designed to solve fractional-order differential equations efficiently. The available solutions are based on product-integration rules, predictor–corrector algorithms, and the Newton-Raphson method. The package covers solutions for one-dimensional equations with orders of positive real numbers. Fo...

Although knowledge of the role of the oral microbiome in ischemic stroke is steadily increasing, little is known about the multi-kingdom microbiota interactions and their consequences. We enrolled participants from a prospective multicentre case–control study and investigated multi-kingdom microbiome differences using saliva metagenomic datasets (n...

Stool consistency explains a large proportion of inter-individual variation in gut microbiota and represents a useful measure of gut transit time, which is pivotal for bacterial metabolism and vice versa. However, in infants and small children, a detailed understanding of how gut microbiota and the metabolome associate with stool consistency is lac...

The early gut microbiota composition is fundamentally important for piglet health, affecting long-term microbiome development and immunity. In this study, the gut microbiota of postparturient dams was compared with that of their offspring in three Finnish pig farms at three growth phases. The differences in fecal microbiota of three study developme...

Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15...

Background Gingivitis, i.e. inflammation of the gums, is often induced by dental plaque. However, its exact link to the oral microbiota remains unclear. Methods In a case-control study involving 120 participants, comprising 60 cases and 60 controls (mean age (SD) 36.6 (7.6) years; 50% males), nested within a prospective multicentre cohort study, w...

Ecological memory refers to the influence of past events on an ecosystem’s response to external or endogenous changes. Whereas memory’s contribution to ecosystem dynamics is well recognized, its role in microbial community dynamics has gained limited attention. Quantitative models of microbial communities have recently shown how resilience and mult...

The gut microbiota is vital for human body development and function. Its development in early life is influenced by various environmental factors. In this randomized controlled trial, the gut microbiota was obtained as a secondary outcome measure in a study on the effects of one hour of daily skin-to-skin contact (SSC) for five weeks in healthy ful...

Manipulative behaviour that consists of touching or close contact with ears or tails of pen mates is common in pigs and can become damaging. Manipulative behaviour was analysed from video recordings of 45-day-old pigs, and 15 manipulator-control pairs (n = 30) were formed. Controls neither received nor performed manipulative behaviour. Rectal faeca...

Background In Indian culture, extended families have symbolized our tradition. Families often encompass members spanning multiple generations cohabiting the same household, thereby sharing ethnicity, genetics, dietary habits, lifestyles, and living conditions. The joint or extended family setup provides an opportunity to compare variations in micro...

The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationship...

Background Studies indicate that gut microbiota is related to neurodevelopmental and behavioral outcomes. Accordingly, early gut microbiota composition (GMC) has been linked to child temperament, but research is still scarce. The aim of this study was to examine how early GMC at 2.5 months is associated with child negative and fear reactivity at 8...

Background Dyslipidemia is treated effectively with statins, but treatment has the potential to induce new-onset type-2 diabetes. Gut microbiota may contribute to this outcome variability. We assessed the associations of gut microbiota diversity and composition with statins. Bacterial associations with statin-associated new-onset type-2 diabetes (T...

The notions of change, such as birth, death, growth, evolution and longevity, extend across reality, including biological, cultural and societal phenomena. Patterns of change describe how success and composition of every entity, from species to societies, vary across time. Languages develop into new languages, music and fashion continuously evolve,...

Background Reports regarding the presence of bacteria in the fetal environment remain limited and controversial. Recently, extracellular vesicles secreted by the human gut microbiota have emerged as a novel mechanism for host-microbiota interaction. We aimed to investigate the presence of bacterial extracellular vesicles in the fetal environment d...

The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed...

Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model interpretation, and the extraction of biological information from the results. To assist decision-making, we offer a set of recommenda...

Multi-omics has opened new avenues for non-invasive risk profiling and early detection of complex diseases. Both polygenic risk scores (PRSs) and the human microbiome have shown promise in improving risk assessment of various common diseases. Here, in a prospective population-based cohort (FINRISK 2002; n=5,676) with ~18 years of e-health record fo...

Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metage...

Early-life gut microbiome-metabolome crosstalk has a pivotal role in the maintenance of host physiology. However, our understanding on early-life gut microbiome-metabolome maturation trajectories in humans remains limited. This study aims to explore the longitudinal patterns of gut metabolites during early life, and how they are related to gut micr...

Microbiomes never stop changing. Their compositions and functions are shaped by the complex interplay of intrinsic and extrinsic drivers, such as growth and migration rates, species interactions, available nutrients and environmental conditions. Mathematical models help us make sense of these complex drivers and intuitively explain how, why and whe...

To develop effective strategies for controlling the spread of the virus and potential future outbreaks, a deep understanding of disease transmission dynamics is crucial. This study proposes a modification to existing mathematical models used to describe the transmission dynamics of COVID-19 with environmental pathogens, incorporating a variable pop...

The recent outbreaks of Ebola encourage researchers to develop mathematical models for simulating the dynamics of Ebola transmission. We continue the study of the models focusing on those with a variable population. Hence, this paper presents a compartmental model consisting of 8-dimensional nonlinear differential equations with a dynamic populatio...

Aims: Deep metagenomics offers an advanced tool for examining the relationship between gut microbiota composition and function and the onset of disease; in this case, does the composition and function of gut microbiota during pregnancy differ in women who develop prediabetes and those who do not at two-year postpartum, and whether the gut microbio...

Background: Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown. Methods: We examined the associations of prevalent and incide...

Introduction: Rodent studies have addressed the importance of early life gut microbiota in the development of emotional and social functioning. Studies in human infants are still scarce, but associations with cognition and temperament have been reported. Neuroimaging studies have linked the amygdala with fecal microbiota diversity in infants, but c...

Background: Preterm children with their aberrant gut microbiota and susceptibility to infections and inflammation constitute a considerable target group for probiotic therapy to generate the age-appropriate healthy microbiota. Methods: 68 preterm neonates were randomized into five intervention groups: Beginning from the median age of 3 days, 13...

Introduction Aberrations in circulating metabolites have been associated with diabetes and cardiovascular risk. Objectives To investigate if early and late pregnancy serum metabolomic profiles differ in women who develop prediabetes by two years postpartum compared to those who remain normoglycemic. Methods An NMR metabolomics platform was used t...

Implementing and executing numerical algorithms to solve fractional differential equations has been less straightforward than using their integer-order counterparts, posing challenges for practitioners who wish to incorporate fractional calculus in applied case studies. Hence, we created an open-source Julia package, FdeSolver, that provides numeri...

Background: The gut-lung axis is generally recognized, but there are few large studies of the gut microbiome and incident respiratory disease in adults. Objectives: To investigate the association and predictive capacity of the gut microbiome for incident asthma and chronic obstructive pulmonary disease (COPD). Methods: Shallow metagenomic sequ...

A broad range of natural and social systems from human microbiome to financial markets can go through critical transitions, where the system suddenly collapses to another stable configuration. Anticipating such transition early and accurately can facilitate controlled system manipulation and mitigation of undesired outcomes. Generic data-driven ind...

The randomized controlled Special Turku Coronary Risk Factor Intervention Project (STRIP) has completed a 20-year infancy-onset dietary counselling intervention to reduce exposure to atherosclerotic cardiovascular disease risk factors via promotion of a heart-healthy diet. The counselling on, e.g., low intake of saturated fat and cholesterol and pr...

Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent modeling studies have shown ho...

Objective: Previous studies on the association between metabolic biomarkers and hypertension have been limited by small sample sizes, low number of studied biomarkers, and cross-sectional study design. In the largest study to date, we assess the cross-sectional and longitudinal associations between high-abundance serum biomarkers and blood pressur...

This report has been prepared by the “Bibliographical Data” Working Group of the DARIAH-ERIC consortium, which develops public digital research infrastructure for the arts and humanities. The Group consists of more than 30 members from 15 countries, most of whom are researchers and curators in the public sector who are engaged in bibliographical da...

The identification of robust and generalizable biomarkers based on microbial abundance data is a challenging task. An algorithm shows an enhanced classification performance by quantifying shifts in microbial co-abundances.

A broad range of natural and social systems from human microbiome to financial markets can go through critical transitions, where the system suddenly collapses to another stable configuration. Critical transitions can be unexpected, with potentially catastrophic consequences. Anticipating them early and accurately can facilitate controlled system m...

Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution.

Background The gut-lung axis is generally recognized, but there are few large studies of the gut microbiome and incident respiratory disease in adults. Objectives3 To investigate the associations between gut microbiome and respiratory disease and to construct predictive models from baseline gut microbiome profiles for incident asthma or chronic ob...

The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well. The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for th...

Background Human skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, th...

Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host‐associated and environment...

Animal models suggest that the gut microbiota can influence cognitive development and functioning via various pathways. In line with that, a first human study found associations between infant fecal microbiota composition and cognition at 2 years of age. This longitudinal study investigated whether fecal microbiota composition in infancy and childh...

The gut microbiome has shown promise as a predictive biomarker for various diseases. However, the potential of gut microbiota for prospective risk prediction of liver disease has not been assessed. Here, we utilized shallow shotgun metagenomic sequencing of a large population-based cohort (N > 7,000) with ∼15 years of follow-up in combination with...

Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (preval...

OBJECTIVE To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort. RESEARCH DESIGN AND METHODS We collected fecal samples from 5,572 Finns (mean age 48.7 years; 54.1% women) in 2002 who were followed up for incident type 2 diabetes until 31 Decemb...

Objective: Previous studies on the association between metabolic biomarkers and hypertension have been limited by small sample sizes, low number of studied biomarkers, and cross-sectional study design. In the largest study to date, we assess the cross-sectional and longitudinal associations between high-abundance serum biomarkers and blood pressur...

OBJECTIVE: To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort. RESEARCH DESIGN AND METHODS: We collected fecal samples of 5 572 Finns (mean age 48.7 years, 54.1% women) in 2002 who were followed up for incident type 2 diabetes until Dec 31 st...

• Ecological communities and other complex systems can undergo abrupt and long-lasting reorganization, a regime shift, when deterministic or stochastic factors bring them to the vicinity of a tipping point between alternative states. Such changes can be large and often arise unexpectedly. However, theoretical and experimental analyses have shown th...

The number of publicly available microbiome samples is continually growing. As dataset size increases, bottlenecks arise in standard analytical pipelines. Faith’s phylogenetic diversity is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's Phylogene...

Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent studies have shown how interac...

Eighteenth Century Collections Online (ECCO) is the most comprehensive dataset available in machine-readable form for eighteenth-century printed texts. It plays a crucial role in studies of eighteenth-century language and it has vast potential for corpus linguistics. At the same time, it is an unbalanced corpus that poses a series of different prob...

Estimating resilience in complex systems Resilience is an important concept in the study of critical transitions and tipping points in complex systems and is defined by the size of the disturbance that a system can endure before tipping into an alternative stable state. Nevertheless, resilience has proved resistant to measurement. Arani et al. show...