Biology subjects

Kallonen, T.

Publications and source records attributed to Kallonen, T..

10 recordsLinked to original sources

bioRxiv2025

Temporal Associations Between Human Milk Metabolites and the Infant Gut Microbiome and metabolome

IntroductionHuman milk is vital in establishing a healthy infant gut microbiome. Gut microbes and their metabolites are important for host development. However, our understanding of how milk metabolites are connected to the gut microbiome and metabolome in early-life remains limited. We aimed to investigate associations between the human milk metabolome and the gut microbiome in infancy. MethodsThe fecal and milk samples were collected at 2.5 (n=283), 6 (n=129) and 14 (n=65) months of age. Gut microbiota was analyzed with amplicon sequencing, the gut metabolome was analyzed with gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry, and milk metabolites were analyzed with proton nuclear magnetic resonance. ResultsBifidobacterium and other butyrate producers were associated with ethanolamine and methionine level in the milk, in a time-dependent manner. Elevated milk fucosylated oligosaccharide, LNFP-I and caprylate concentrations were positively associated with secondary bile acid levels following the introduction of solid foods. Additionally, acidic oligosaccharides 3-SL and 6-SL were positively associated with long-chain carbohydrates prior to solid food introduction, however negatively associated thereafter. ConclusionOur results highlight that milk metabolites are associated with biologically relevant gut microbial metabolites. Only limited associations were observed between milk composition and the microbiome, which differed between early and late infancy. This suggests milk metabolome may differentially influence microbial metabolism depending on dietary diversity and/or the maturity of the microbiome. ImportanceIts essential to raise awareness about breastfeeding and its variety of health benefits. Expanding our understanding of how human milk small molecules with potential bioactivity interact with the gut microbiome can help highlight these positive effects. Exploratory studies of human milk composition with gut microbial metabolites may support achieving this goal. Furthermore, understanding of biological effects of different components in human milk is important, and it can help to develop strategies to ensure optimal growth and development of an infant regardless of the breastfeeding status of the child.

microbiology↗

bioRxiv2025

Faecal transplantation from exuberant toddlers increases exploratory behaviour in rats

BackgroundBehavioural phenotypes have previously been transferred via faecal microbiota transplantation (FMT) from patients with psychiatric disorders to rodents. Studies indicate that the gut microbiota composition may be linked to certain temperament traits, defined as biologically-based differences in emotional reactivity and self-regulation. Here, we aimed to determine if the gut microbiota plays a role in temperament using an FMT approach. We focused on the temperament traits of exuberance, defined as positive reactivity, decreased behavioural inhibition, and high behavioural approach tendencies. MethodsFaeces from 2.5-year-old toddlers from FinnBrain Birth Cohort Study with high exuberance/approach or high behavioural inhibition in the LabTAB bubbles-episode was transferred to juvenile male Sprague Dawley rats (age 22/23 days). Behaviour of the rat recipients (n=53) was assessed using the novel non-social arena, novel social arena, hole board test for exploratory behaviour, social approach-avoidance test, and forced swim test. The faecal pellets collected from the rodents were analyzed with 16s rRNA sequencing and faecal samples from the sample of toddlers (which included the donors, n=176) were analysed using short-read metagenomic sequencing. The striatum and prefrontal cortex from the rodents brains were analysed post-mortem using RNAseq. ResultsMicrobiome from toddlers with high exuberance traits induced increased exploratory behaviour compared to vehicle-controls and rats receiving faeces from inhibited toddlers. Locomotor activity, social, and depressive-like behaviour remained unaffected. We noted a downregulation of the dopamine synapse pathway within the striatum of the rats that received faeces from the inhibited trait donors compared with vehicle-controls. Faecal microbiota of rats receiving faeces from the same donor resembled more each other than rats from a different cage. Clostridium species AM29 11AC in toddler microbiome was positively related to exuberance, but there were no cross-sectional associations between faecal metabolites in the human sample. ConclusionsFMT from exuberant toddlers lead to altered exploratory-related behaviour in rats.

microbiology↗

bioRxiv2025

Longitudinal dynamics of gut plasmidome and antibiotic resistance during antibiotic therapy: a case report

The human gut microbiome is composed of diverse microbes, and its association with human health is well-recognized. Antibiotic therapies for treating infectious diseases often mediate adverse influences on gut microbial ecosystems. Further, ESBL (extended-spectrum beta-lactamase)-producing bacteria potentially residing in the gut benefit from antibiotic-induced environmental changes via positive selection for resistance traits. As antimicrobial resistance (AMR) genes are often harbored by mobile plasmids, the importance of these extrachromosomal mobile genetic elements during antibiotic exposure is evident. However, there is still a knowledge gap in how microbiomes respond to antibiotic treatment especially in terms of plasmid carriage and how gut plasmid populations evolve following and revive after antibiotic therapy. To address these questions, in this case report we investigated the changes in plasmid population in the gut microbiome of a single ESBL-carrying patient during antibiotic therapy for uncomplicated acute appendicitis. Employing longitudinal sampling, we collected E. coli strains and performed metagenomic analysis before, during, and after the treatment. Our findings indicate that the antibiotic treatment is associated with a transient alteration in the microbial composition, AMR profile, and plasmid population. An extensive but temporary domination of ESBL-E. coli within the gut microbiome was observed parallel to the ongoing antibiotic treatment. However, this was not sustained in the follow-up period, indicating a slight restoration of both the microbial composition and the plasmid population. The research underscores the temporary impact of antibiotic therapy on the dynamics of the gut plasmidome which essentially mediate the spread of AMR within the gut microbiome.

microbiology↗

bioRxiv2023

Comparative metabolomics and microbiome analysis of Ethanol vs. OMNImet/gene GUT fecal stabilization

Metabolites from feces provide important insights into the functionality of the gut microbiome. As immediate freezing is not always feasible in gut microbiome studies, there is a need for sampling protocols that provide stability of the fecal metabolome and microbiome at room temperature (RT). For this purpose, we investigated the stability of various metabolites and the microbiome (16S ribosomal RNA) in feces collected in 95% ethanol (EtOH) or OMNImet(R)*GUT/ OMNIgene(R)*GUT. To simulate in field-collection scenarios, the samples were stored at different temperatures at varying durations (24h +4{degrees}C, 24h RT, 36h RT, 48h RT, and 7 days RT), and compared to aliquots immediately frozen at -80{degrees}C. We applied several targeted and untargeted metabolomics platforms to measure lipids, polar untargeted metabolites, endocannabinoids, short chain fatty acids (SCFAs), and bile acids (BAs). We found that SCFAs in the non-stabilized samples increased over time, while a stable profile was recorded in sample aliquots stored in 95% EtOH and OMNImet(R)*GUT. When comparing the metabolite levels between fecal aliquots stored at room temperature and at +4{degrees}C, we detected several changes in microbial metabolites, including multiple BAs and SCFAs. Taken together, we found that storing fecal samples at room temperature and stabilizing them in 95% EtOH yielded metabolomic results comparable to flash freezing. We also found that overall composition of the gut microbiome did not vary significantly between different storage types. However, there were notable differences observed in alpha diversity. Taken together, the stability of the metabolome and microbiome in 95 % EtOH provided similar results as the validated commercial collection kits OMNImet(R)*GUT and OMNIgene(R)*GUT, respectively. IMPORTANCEThe analysis of the gut metabolome and microbiome requires the separate collection of fecal specimens using conventional methods or commercial kits. However, these approaches can potentially introduce sampling errors and biases. In addition, the logistical requirements of studying large human cohorts have driven the need for home collection and transport of human fecal specimens at room temperature. By adopting a unified sampling approach at room temperature, we can enhance sampling convenience and practicality, leading to a more precise and comprehensive understanding of gut microbial function. However, the development and applications of such unified sampling systems still face limitations. The results presented in this study aim to address this knowledge gap by investigating the stability of metabolites and the microbiome (16S ribosomal RNA) from fecal samples collected using 95% EtOH, in comparison to well-established commercial collection kits for fecal metabolome (OMNImet(R)*GUT) and microbiome (OMNIgene(R) *GUT) profiling. Additionally, we perform a comparative analysis of various platforms and metabolomic coverage using matrices containing ethanol, evaluating aspects of sensitivity, robustness, and throughput.

biochemistry↗

bioRxiv2021

One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment

The Klebsiella group is highly diverse both genetically and ecologically, being commonly recovered from humans, livestock, plants, soil, water, and wild animals. Many species are opportunistic pathogens, and can harbour diverse classes of antimicrobial resistance (AMR) genes. K. pneumoniae is responsible for a high public-health burden, due in part to the rapid spread of health-care associated clones that are non-susceptible to carbapenems. Klebsiella thus represents a highly pertinent taxon for assessing the risk to public health posed by animal and environmental reservoirs. Here we report an analysis of 6548 samples and 3,482 genome sequences representing 15 Klebsiella species sampled over a 15-month period from a wide range of clinical, community, animal and environmental settings in and around the city of Pavia, in the northern Italian region of Lombardy. Despite carbapenem-resistant clones circulating at a high frequency in the hospitals, we find no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside of the clinical environment. The non-random distribution of species and strains across sources point to ecological barriers that are likely to limit AMR transmission. Although we find evidence for occasional transmission between settings, hierarchical modelling and intervention analysis suggests that direct transmission from the multiple non-human (animal and environmental) sources included in our sample accounts for less than 1% of hospital disease, with the vast majority of clinical cases originating from other humans.

microbiology↗

bioRxiv2020

The binding mechanism of Streptococcus suis accessory virulence factor and adhesin SadP to globotetraosylceramide

Streptococcus suis is part of the pig commensal microbiome and a major pathogen causing pneumonia and meningitis in pigs and occasionally also zoonotic meningitis. According to genomic analysis, S. suis is divided into asymptomatic carriage, respiratory and systemic strains with distinct genomic signatures. The virulence factor S. suis adhesin P (SadP) recognizes the galabiose Gal1-4Gal-oligosaccharide. Based on its oligosaccharide fine specificity, SadP can be divided into subtypes PN and PO. We show here that subtype PN is distributed in the systemic strains that cause meningitis, whereas type PO is found in asymptomatic carriage and respiratory strains. Both types of SadP are shown to predominantly bind to pig lung globotriaosylceramide (Gb3). However, SadP adhesin from systemic subtype PN strain also binds to globotetraosylceramide (Gb4). Mutagenesis studies of the galabiose-binding domain of type PN SadP adhesin showed that the amino acid asparagine-285, which is replaced by an aspartate residue in type Po SadP, was required for binding to Gb4 and, strikingly, it was also required for interaction with the glycomimetic inhibitor phenylurea-galabiose. Molecular dynamics simulations provided further insight into the role of Asn-285 for Gb4 and phenylurea-galabiose binding, suggesting additional hydrogen bonding to terminal GalNAc of Gb4 and urea-group. Thus, the Asn-285-mediated molecular mechanism of type PN SadP binding to Gb4 could be used as a candidate to selectively target S. suis in invasive systemic disease without interfering with commensal strains, which may open up new venues for developing intervention strategies against this pathogen.

microbiology↗

bioRxiv2020

Genomic Epidemiology with Mixed Samples

Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, skipping the colony pick step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.

bioinformatics↗

bioRxiv2019

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions

BackgroundAntimicrobial resistance (AMR) is highly prevalent in low- and middle-income countries (LMIC). International travel contributes substantially to the global spread of intestinal multidrug-resistant gram-negative (MDR-GN) bacteria. Of the 100 million annual visitors to LMIC, 30-70% become colonized by MDR-GN bacteria. The phenomenon has been well documented, but since sampling has only been conducted after travelers return home, data on the actual colonization process are scarce. We aimed to characterize colonization dynamics by exploring stool samples abroad on a daily basis while visiting LMIC. MethodsA group of 20 European volunteers visiting Lao Peoples Democratic Republic for three weeks provided daily stool samples and filled in daily questionnaires. Acquisition of extended-spectrum beta-lactamase-producing gram-negative bacteria (ESBL-GN) was examined by selective stool cultures followed by whole-genome sequencing (WGS) of isolates. ResultsWhile colonization rates were 70% at the end of the study, daily sampling revealed that all participants had acquired ESBL-GN at some time point during their overseas stay, the colonization status varying day by day. WGS analysis ascribed the transient pattern of colonization to sequential acquisition of new strains, resulting in a loss of detectable colonization by the initial MDR-GN strains. All but one participant acquired multiple strains (n=2-7). Of the total of 83 unique strains identified (53 E. coli, 10 Klebsiella, 20 other ESBL-GN species), some were shared by as many as four subjects. ConclusionsThis is the first study to characterize in real time the dynamics of acquiring MDR-GN during travel. Our data show multiple transient colonization events indicative of constant microbial competition.

microbiology↗

bioRxiv2018

Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli

Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multi-drug resistant (MDR) strains of extra-intestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution towards separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonisation and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen.

microbiology↗

bioRxiv2018

High-resolution sweep metagenomics using ultrafast read mapping and inference

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP method for identifying and estimating the relative abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our method facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

bioinformatics↗