APC Microbiome Institute

Poly-γ-glutamic acid (γ-PGA) is a valuable biopolymer with diverse industrial applications, produced naturally by several Bacillus species. The dairy environment is an under-explored niche for identifying efficient, food-grade γ-PGA producers. In this study, four legacy dairy-derived Bacillus licheniformis strains: DPC3803, DPC6338, DPC6339, and DPC6340, producing high γ-PGA titres were examined using whole genome sequencing (WGS) and comparative genomic analysis to evaluate their suitability for future industrial applications. The genomes ranged from 4.19 to 4.29 Mb with an average GC content of 45.8–46.2%. Pangenome analysis of the four strains, together with 51 publicly available B. licheniformis genomes, identified 12,415 gene clusters, of which 18.9% and 81.1% were core and accessory genes respectively. Average nucleotide identity (ANI) analysis demonstrated >99% sequence identity among all 55 B. licheniformis genomes, despite their isolation from diverse environments, indicating strong genomic conservation within the species. Experimental validation confirmed γ-PGA production by all four strains, with maximum titres (g/L) of 43.27 ± 1.49, 59.54 ± 4.33, 27.93 ± 1.87, and 47.74 ± 0.19 for DPC3803, DPC6338, DPC6339, and DPC6340, respectively. Genomic screening revealed multiple γ-PGA metabolism and CAZyme-encoding genes, as well as unique secondary metabolite clusters with potential antimicrobial activity. Although no plasmids or virulence factors were detected, twenty-one prophages were identified, sharing no significant homology with known cultivated phages, and a single β-lactamase gene suggested intrinsic resistance to β-lactams. These findings highlight the genomic and functional potential of these dairy-derived B. licheniformis as efficient, food-grade candidates for industrial γ-PGA production.

Alzheimer disease (AD) and aging have similar molecular mechanisms that are affected by genetic as well as environmental variables. Based on current research, gut microbiomes contribute to age-specific biological processes and play an essential role in maintaining host homeostasis. Several molecular processes, including the host DNA methylation mechanism, are affected by microbially derived metabolites such as short-chain fatty acids, folate, and choline. This interaction establishes a mechanistic causal relationship that further shapes gene expression, inflammatory balance, and neuronal function in aging and related diseases. In this review, we looked at recent research showing how gut dysbiosis and its associated metabolites impact DNA methylation, which consequently contributes to disease progression in AD and aging. We also talked about how the DNA clock and age-associated methylation drifts can be used for forecasting biological aging. In addition, we discussed recent findings on how microbial and diet-based interventions may restore the methylation patterns that might be involved in aging and neurodegenerative processes. We also implicated the possible use of methylation-based biomarkers in the diagnosis of AD. Additionally, we have also explored the potential therapeutic benefits of using microbiome modulators, dietary modifications, and pharmacological interventions. Next, we highlighted the importance of multiomics and longitudinal studies to build the causal connection underlying methylation dynamics and microbial changes in neurodegeneration. Altogether, this review highlights the potential of the microbiome-methylation axis as an approach to understanding aging and establishing precision strategies to maintain cognitive health. SIGNIFICANCE STATEMENT: This review explores the interplay between DNA methylation and gut microbiota in aging and Alzheimer's disease. It highlights the gut-brain axis and summarizes recent findings on microbiome-driven epigenetic changes and metabolites influencing cognitive decline. The review also emphasizes microbiome-targeted therapeutic strategies for age-related disorders. Overall, it integrates current molecular insights with emerging approaches for the detection, prevention, and management of Alzheimer's disease and associated cognitive challenges.

The partners of an ecological association tend to copy the biological system of their hosts. We hypothesized that microorganisms, particularly pathogens, have acquired the ability to express short peptides (pathoPEPs) homologous to host miPEPs, thus modulating the expression of the corresponding host microRNA (miRNA) and the function of miRNA-targeted genes. The pathosystem involving interactions between Brassica napus and its pathogen Plasmodiophora brassicae was studied. The data set contains RNA-seq and ribosomal profiling from two plant genotypes inoculated with one pathogen isolate. Using in silico analysis, we identified three putative pathoPEPs produced by P. brassicae and their targeted plant miRNA genes. A link between the level of infection of B. napus by P. brassicae and the expression of pathoPEPs and their targeted miRNA genes was found, with the expression of the latter two being inversely related. Finally, we identified differential expression and translation of genes predicted to be targets of pathoPEP-regulated miRNAs. These genes, involved in auxin pathway, immune defense, root architecture, or carbohydrate metabolism, are thought to enable P. brassicae, through its pathoPEPs, to hijack plant's metabolic pathways (e.g., hormonal pathways, sugar synthesis, root morphology), thereby facilitating its invasion. Using in silico approaches, the involvement of miPEPs from this host-pathogen system as a host post-transcriptional regulatory pathway is described herein for the first time.

Mild cognitive impairment (MCI) is an early stage in the progression toward dementia. Lipids are central to neurodegeneration, yet the biomarker potential of lipidomics from saliva, plasma, and feces remains underexplored. As part of the Microbiome in Aging Gut and Brain (MiaGB) consortium, saliva, plasma, and fecal samples were collected from older adults with MCI and healthy controls. Samples were analyzed by high-performance liquid chromatography coupled with high-resolution mass spectrometry (LC/MS), to profile lipidomic alterations and identify candidate biomarkers. Lipidomic profiling annotated over 200 molecular species spanning five major lipid classes. Compared with controls, MCI patients exhibited increased oxidized triacylglycerols (oxTGs) in saliva, reduced cholesteryl linoleate (CE 18:2) in plasma, and decreased fatty acid esters of hydroxy fatty acids (FAHFAs) in feces. Receiver operating characteristic (ROC) analysis identified α-linolenic acid (FA 18:3), docosapentaenoic acid (FA 22:5), and CE 18:2 as discriminatory metabolites with notable diagnostic performance. Moreover, elevated fecal triacylglycerols containing medium-chain fatty acids (TG-MCFAs) were observed in MCI, suggesting impaired lipid absorption or altered metabolism. This multi-sample lipidomics strategy highlights TG-MCFAs as fecal biomarkers for MCI detection, supporting further mechanistic and longitudinal validation.

The gut microbiome is a transducer of the health effects of many food ingredients because of its ability to convert them into health-impacting compounds. Plant-forward diets and plant ingredients are recognized as health promoting, with recent added impetus provided by the drive to provide consumers with more sustainable protein sources than meat. Soy-based foods are good protein sources, and they contain a variety of other ingredients such as fibre that can impact the microbiome. This review explores the health benefits reported for soy-containing foods and the role of microbiome involvement in health effects. It describes the bi-directional relationship between dietary soy and the human gut microbiome whereby microbial metabolism transforms soy-derived compounds into bioactive forms that influence host physiology, while soy consumption shapes gut microbiota composition and activity. Factors modulating the health effects of soy such as fermentation, bioavailability, and consumers’ individual microbiome configurations are discussed. Current research limitations, including inconsistent methodologies and a lack of longitudinal dietary intervention studies are addressed, as well as the need for multiple omics approaches in microbiome research. Finally, we present an interdisciplinary perspective of the complexity of soy-microbiome interactions, potential for health promotion, and relationship to sustainability.

Methane (CH4) emissions from enteric fermentation in ruminants represent the largest source of anthropogenic agricultural emissions, contributing significantly to global CH4 levels. Enteric CH4 mitigation strategies have been intensively investigated to address the detrimental effects on climate change and ruminant production characteristics. This systematic review investigated whether microbial silage inoculants could reduce CH4 formation in the rumen microbiome, both ex vivo and in vivo, based on available literature. Two independent reviewers conducted a comprehensive search for peer-reviewed articles, without year restrictions, up to January 31, 2024. The search focused on studies reporting CH4 gas production both in vitro and in vivo. Of 434 articles initially identified, only 10 met the quality criteria and were included in the analysis. Among the selected studies, 9 measured CH4 production using in vitro assays, whereas one reported an in vivo trial. The majority of the experiments (70%) were conducted using cattle rumen samples, including the in vivo study involving cattle, the remainder of the experiments used rumen samples obtained from sheep. Ten bacterial species were used as inoculants across the selected studies. Lactobacillus buchneri, used in combination with additives, achieved the highest CH4 reduction at 83%. Lactiplantibacillus plantarum also showed a significant reduction in CH4 output, achieving a 48% decrease. Overall, 80% of the reviewed studies reported a reduction in CH4 production by ruminant microorganisms following the application of silage microbial inoculants. These findings suggest that silage microbial inoculants hold promise as a strategy to mitigate CH4 emissions in livestock. The limited number of studies highlights the need for further research to confirm these results and explore wider applications.

Mounting pressures on global food chains call for an urgent shift towards more sustainable food systems. Several ways to aid this transformation are the reduction of food waste through the valorisation of food processing side streams, and a shift from animal-based to plant-based proteins. As plant-based proteins are gaining popularity as alternatives to dairy and meat due to the rising demand for healthy, natural foods and their ethical appeal, it is essential that the protein quality of novel, alternative protein sources are evaluated. Brewers' spent grain (BSG) is a nutrient-rich brewing by-product which has been upcycled to produce everpro™ Dark Fraction (EDF) and a decolourised protein isolate known as everpro™ Light Fraction (ELF). This study investigates the in vitro protein and amino acid digestibility and in vitro digestible indispensable amino acid score (DIAAS) of EDF and ELF in comparison to pea, soy, and whey protein isolates using the static INFOGEST model. All ingredients demonstrated high digestibility (> 80%), while in vitro DIAAS of 51% and 37% were determined for EDF and ELF, respectively, lower values than the soy or whey proteins, but higher than or comparable to the two pea proteins studied. Differences were observed in the digestibility of individual amino acids in EDF and ELF and the resulting digestible indispensable amino acid ratio (DIAAR) values, indicating that the decolourisation process may be impacting protein quality. Overall, this study highlights how everpro™ ingredients can transform the food industry as alternative protein sources, enabling manufacturers to promote a more sustainable future. • Everpro™ Dark (EDF) and Light Fractions (ELF) are high-protein, low-fat ingredients • EDF and ELF had in vitro digestibilities similar to pea, soy, and whey proteins • In vitro DIAAS values of 51% and 37% were determined for EDF and ELF, respectively • Decolourisation may be impacting the protein quality of ELF • Both ingredients show potential for use in protein-enriched food products

Due to their importance in global ocean ecology and biogeochemistry, much is known about the abundance and diversity of marine microbes and this data informs our studies of microbial genetic variability and niche partitioning. However, much less is known about marine microbes’ vital rates, including phylogenetically-resolved intrinsic growth and mortality. Here, we use cyanobacteria to validate a recently-developed, sequence-based modification of the Landry-Hassett Dilution (LHD) technique, which simultaneously assesses the growth and grazer-induced mortality of microbial subpopulations. Using laboratory cultures, we show that most approaches for quantifying cyanobacterial intrinsic growth yield similar results, providing a foundation for methods comparisons in complex communities. We then leverage these findings to validate the modified LHD approach by sampling from a highly-dynamic, coastal marine ecosystem. We find that the LHD 16S rRNA gene-based method returns the same intrinsic growth as other biomass estimates. Further, field sampling yields distinct intrinsic growth among closely-related lineages of both cyano- and heterotrophic bacteria. While grazer-mediated mortality was less variable, we did observe distinct mortality rates within the broader microbiome, supporting the importance of examining vital rates in subpopulations. This validated methodology (and initial field findings) opens the door to answer fundamental ecological and biogeochemical questions about the microbial oceanography of spatially and temporally-variable coastal and open ocean ecosystems.

Streptococcus suis is a major pig pathogen with zoonotic potential, posing an occupational risk to farmers and meat handlers. We characterized 110 S. suis strains from diseased pigs in Ireland (2005-2022) using whole-genome sequencing to investigate population structure and phage-host dynamics. We identified 15 distinct serotypes, with serotypes 9 and 2 being the most dominant. In silico multi-locus sequence typing revealed high diversity within the collection, identifying several sequence types (STs), including 26 novel STs. Investigation of strain-level genomic clustering using PopPUNK against global S. suis genomes showed that the Irish isolates were phylogenetically dispersed across the broader global S. suis population rather than clustering in a single clonal group. The majority of Irish isolates fall within the ten established pathogenic lineages, including the highly virulent zoonotic lineage 1. A locally persistent clonal lineage was identified among Irish isolates, showing minimal genetic variation over a decade.Prophage analysis revealed novel viral taxa that were interspersed among known streptococcal phages, rather than clustering distinctly. Restriction-modification systems were the predominant anti-viral defence systems identified across genomes. CRISPR-Cas systems were present in limited strains but showed substantial targeting bias toward full-length prophages, indicating ongoing phage pressure. CRISPR spacers matched non-S. suis streptococcal phages, and phylogenomic analysis revealed that Vansinderenvirus phages clustered with S. suis rather than other Streptococcus thermophilus phages, suggesting evolutionary connections between phage lineages infecting different streptococci.This study presents the first comprehensive genomic characterization of S. suis in Ireland, revealing a diverse population with significant implications for animal and human health.