Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics.

: Antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics in livestock, offering a sustainable strategy for controlling bacterial pathogens in food production systems. In addition to their direct antimicrobial effects, AMPs play a key role in modulating host-associated microbiomes, influencing both microbial composition and function. Advances in metagenomic sequencing and bioinformatic tools now enable comprehensive exploration of AMP diversity and activity within complex microbial ecosystems.

Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.

Metabolic health improvements in response to exercise and energy restriction may be mediated by the gut microbiome, yet causal evidence in humans remains limited. We used a 3-week exercise and energy restriction intervention to examine changes to the gut microbiome in otherwise healthy sedentary men and postmenopausal women with overweight/obesity. Intervention participants (n = 18) reduced habitual energy intake by 5000 kcal/week and expended 2000 kcal/week in addition to habitual physical activity through treadmill walking at 70% V̇O.

Maternal immune activation and antibiotics affect offspring neurodevelopment, behaviour, and microbiome.

exposure to an increased level of maternal inflammation or a disrupted maternal gut microbiome during pregnancy have been linked to several neurodevelopmental disorders in the offspring. Despite the strong links between these two adverse events, few studies looked at the interaction between the maternal gut microbiome and maternal immune activation (MIA) on the neurodevelopmental outcomes in the offspring. Here, we aim to determine if maternal gut microbiome disruption exacerbated the impact of systemic inflammation on brain development, offspring behaviour, and long-term microbiome changes.

Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome.

The infant resistome, the collection of antimicrobial resistance genes (ARGs) of newborns, is critical for gut microbiota establishment. Using metagenomic sequencing data, we analyzed various 1-week and 1-month postpartum samples to study infant resistome establishment, ARG transmission, and its impact on functional redundancy of the microbiota. A total of 431 samples were analyzed; infant stools (1-week,  = 119; 1-month,  = 119), maternal stools (1-month postpartum,  = 120), and breastmilk (1-month postpartum,  = 73).

The food-associated resistome is shaped by processing and production environments.

Food production systems may act as transmission routes for antimicrobial-resistant (AMR) bacteria and AMR genes (AMRGs) to humans. However, the food resistome remains poorly characterized. Here 1,780 raw-material (milk, brine, fresh meat and so on), end-product (cheese, fish, meat products and vegetables) and surface (processing, cooling, smoking, ripening and packing rooms) samples from 113 food processing facilities were subjected to whole-metagenome sequencing.

Development of a bio-functional fermented soy beverage supplemented with microbial exopolysaccharides and its effect on the human gut microbiome .

The gut microbiome plays a key role in modulating human health and well-being. Exopolysaccharides (EPS) produced by lactic acid bacteria (LAB) are emerging as novel polymers that could exert a prebiotic effect modification of this microbiome. Thus, incorporation of EPS to enhance food functionality is of interest.

Faecal microbiota and serum metabolome association with equine metabolic syndrome in connemara ponies.

Background: Faecal microbiome and serum metabolome have been studied in human medicine to provide a better understanding of metabolic derangements including diabetes; however, equivalent studies in equine medicine are limited. This was a case-control study conducted to identify differences in faecal microbiota composition and concurrent serum metabolite patterns between metabolically normal Connemara ponies and those with Equine Metabolic Syndrome (EMS). Thirty privately owned Connemara ponies (15 EMS and 15 controls) were included in the study.

A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset.

Developing a better understanding of the genomic and metabolic features of acetic acid bacteria (AABs) has the potential to facilitate an improvement of the taste or flavor of fermented foods. Here, we conducted a high-resolution analysis of AABs present in fermented foods based on the investigation of 337 high-quality metagenomic-assembled genomes (MAGs) recovered from 223 metagenomic samples. Firstly, by integrating these MAGs, we built a phylogenetic tree of high-quality MAGs using GTDB-Tk.

Gene-trait matching among strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster.

In contrast to other human-associated bifidobacteria, is commonly classified as an opportunistic pathogen as its presence in the oral cavity has been associated with the development of dental caries. While is frequently isolated from the oral cavity of children with caries, recent microbiome investigations and preliminary genomic analyses have suggested that this species is also adapted to colonize the gastrointestinal tract. Understanding the genetic and metabolic adaptations that enable this flexible colonization ability is crucial to clarify its role in human health and disease.

Effects of feeding a simulated waste milk on growth, health, fecal microbiota, and antibiotic resistance in dairy heifer calves.

Feeding waste milk, a common practice in dairy farming, exposes calves to subtherapeutic levels of antimicrobials, potentially contributing to antibiotic resistance-a growing concern globally. Many dairy farmers, including those in Ireland, continue this practice, feeding waste milk from antibiotic-treated cows to calves. Although previous studies have linked waste milk feeding to changes in calf growth and health during the preweaning period, its effects postweaning remain unclear.

OPTIMATRIX v2.0: Optimised protocol to mitigate microbial blooms in the micro-Matrix bioreactor platform used as an human distal colon model.

We previously reported optimisation of the methodology to mitigate blooms and associated loss of microbial diversity when using the micro-Matrix bioreactor platform as an model of the human distal colon. Here, we provide further critical insights that we have gained in this regard through follow-up experiments. We tested four separate faecal fermentation media compositions for the purposes of such distal colon model experiments and found that the media composition described by MacFarlane is the most suitable for mitigating such microbial blooms, and concurrently, maintaining microbial diversity.

The effects of offering adequate-quality or high-quality colostrum on the passive immunity, health, growth, and fecal microbiome development of dairy heifer calves.

Colostrum quality is influenced by multiple factors, including its microbial load, which is determined by the cleanliness of collection and storage conditions. Additionally, the dam's diet and immune status play a crucial role in shaping colostrum quality by affecting IgG concentrations. Whereas many factors contribute to colostrum quality, this study will specifically use IgG content as the primary measure of quality.

Cottage cheese, a relatively underexplored cultured dairy product with potential health benefits?

Cottage cheese (CC) is a member of the "fresh cheese" family of cheeses and is widely consumed due to its culinary versatility and some perceived health benefits. However, the evidence of direct health effects of CC is not well established. This review describes the production and nutritional characteristics of CC, before exploring the evidence of health effects from human intervention, , and models.

Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.

SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health.

Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.

The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces.

The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.

Water kefir (WK) is an artisanal fermented beverage made from sugary water, optional fruits and WK grains. WK grains can be reused to start new fermentations. Here we investigate the microbial composition and function of 69 WK grains and their ferments by shotgun metagenomics.

Bactofencin A Displays a Delayed Killing Effect on a Clinical Strain of Which Is Greatly Accelerated in the Presence of Nisin.

Bacteriocins can be considered a novel source of natural alternatives to antibiotics or chemical food additives with the potential to fight against clinical and food pathogens. A number have already been commercialised as food preservatives, but they also have the potential to treat drug-resistant clinical pathogens and can play a role in immune modulation. To achieve their full potential, an understanding of their mode of action is required.

Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.

Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time.

Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.

Rapid advancements in long-read sequencing have facilitated species-level microbial profiling through full-length 16S rRNA sequencing (~ 1500 bp), and more notably, by the newer 16S-ITS-23S ribosomal RNA operon (RRN) sequencing (~ 4500 bp). RRN sequencing is emerging as a superior method for species resolution, exceeding the capabilities of short-read and full-length 16S rRNA sequencing. However, being in its early stages of development, RRN sequencing has several underexplored or understudied elements, highlighting the need for a critical and thorough examination of its methodologies.

From human to superhuman: the impact of the microbiome on physiology.

The complex microbial community residing in the human gut has long been understood to regulate gastrointestinal physiology and to participate in digestive diseases, but its extraintestinal actions and influences are increasingly recognized. This article discusses bidirectional interactions between the gut microbiome and athletic performance, metabolism, longevity and the ability of the gut-brain axis to influence cognitive function and mental health.

Pediococcus acidilactici CECT 9879 (pA1c®) and heat inactivated pA1c® (pA1c® HI) ameliorate gestational diabetes mellitus in mice.

Aims: Gestational diabetes mellitus (GDM) is the most common complication of pregnancy and is known to be associated with an increased risk of postpartum metabolic disease. Based on the important role that the intestinal microbiota plays in blood glucose regulation and insulin sensitivity, supplementation of probiotic and postbiotic strains could improve glucose metabolism and tolerance in GDM.

Main Methods: 56 4-week-old female C57BL/6J-mice were divided into 4 groups (n = 14 animals/group): control (CNT), high-fat/high-sucrose (HFS), pA1c® alive (pA1c®) and heat-inactivated pA1c® (pA1c®HI).

Preterm-birth-prevention with Lactobacillus crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).

Introduction: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp.

A gut-derived produces the novel nisin variant designated nisin G and inhibits in a model of the human distal colon microbiome.

is a human pathogen associated with intestinal conditions including colorectal cancer. Screening for gut-derived strains that exhibit anti-. activity revealed DPC6487 as a strain of interest.