Antimicrobial resistance (AMR) represents a critical global health challenge, with low- and middle-income countries (LMICs) disproportionately affected due to limited surveillance capacity. Advances in microbial genomics offer powerful tools for AMR detection and monitoring; however, translating these technologies into sustainable, policy-relevant surveillance systems in resource-constrained settings remains challenging. This review synthesises current approaches to genomic surveillance of AMR in LMICs and presents Bangladesh as a case study to illustrate how genomic, environmental, and clinical data can be integrated within a One Health framework. We examine key barriers to implementation, including laboratory infrastructure, bioinformatics capacity, data governance, and cross-sector coordination, alongside emerging opportunities for capacity building and regional collaboration. Using Bangladesh as a case study, we highlight practical pathways for embedding genomic surveillance into national AMR strategies, integrating human, animal, and environmental reservoirs of antibiotic resistance. We argue that genomic surveillance can move beyond data generation to inform infection prevention, antibiotic stewardship, and public health decision making when supported by context-appropriate infrastructure and interdisciplinary engagement. By focusing on operational and translational considerations rather than technology alone, this review provides actionable insights for microbiologists, public health practitioners, and policymakers seeking to strengthen AMR surveillance systems in LMICs through a One Health approach.

Antimicrobial resistance (AMR) is increasingly recognised as a One Health challenge in which environmental reservoirs play an important role in the persistence and dissemination of resistance genes. Despite growing recognition that environmental antimicrobial resistance is a critical component of the One Health challenge, the pathways through which antimicrobial resistance genes (ARGs) move between environmental systems and human populations remain incompletely characterised, particularly in low- and middle-income countries where environmental exposures are greatest and surveillance capacity is limited. This review synthesises current knowledge on environmental resistomes across soil, water, sediment and groundwater systems, with a focus on metagenomic and quantitative analytical approaches that have transformed environmental AMR surveillance. Unlike traditional culture-based methods, metagenomics enables comprehensive, culture-independent profiling of microbial communities and their associated resistomes, allowing detection of both known and previously uncharacterised resistance genes, as well as insights into their genetic context and mobility. This has significantly advanced our ability to characterise environmental reservoirs and infer potential transmission pathways at ecosystem scale. Using Bangladesh as an illustrative example of environmental exposure dynamics in rapidly urbanising low- and middle-income settings, we examine how contaminated urban waterways, wastewater discharge, agricultural practices, and seasonal hydrological processes-including monsoon-driven flooding-create interconnected transmission pathways linking environmental, animal, and human microbiomes. We also consider how co-selection pressures from heavy metals and other environmental contaminants contribute to the persistence and amplification of antimicrobial resistance beyond antibiotic-driven selection alone. These dynamics are further intensified by dense surface water networks, strong hydrological connectivity, and limited wastewater treatment infrastructure, which together create high-intensity human-environment interfaces and facilitate large-scale redistribution of antimicrobial resistance genes across environmental compartments. Taken together, these features make Bangladesh an analytically distinctive and tractable model system for understanding environmental AMR dynamics, with relevance to comparable deltaic and monsoon-influenced regions in South and Southeast Asia. Key methodological challenges-including the gap between ARG detection and clinical risk interpretation, biases in resistance gene databases, sampling limitations, and the lack of harmonised environmental surveillance frameworks-are examined alongside emerging tools such as long-read sequencing, functional metagenomics and artificial intelligence-assisted bioinformatic analysis. Finally, we propose an integrated One Health framework linking environmental metagenomics, global surveillance systems and policy interventions to support harmonised, data-driven monitoring and mitigation of environmental AMR across interconnected ecosystems.

Antimicrobial resistance (AMR) poses a critical threat to global health, food security, and economic development. India is a major hotspot for AMR emergence, driven by high consumption of antimicrobials, often unregulated or used without a prescription. Recognizing this challenge, the India–UK AMR Network Meeting was jointly convened by the University of Leeds, UK, and SRM University-AP, India, to develop a multidisciplinary research network that focuses on integrated perspectives across human health, veterinary sciences, environmental microbiology, social medicine, and bioinformatics within a One Health framework. The meeting was held from January 21 to 23, 2026, at SRM University-AP, Andhra Pradesh, India. This network meeting brought together interdisciplinary experts from India and the United Kingdom to establish this collaborative framework. Key discussions addressed AMR surveillance strategies at the community level across themes such as human, animal, and environmental health. Topics included mechanisms such as cross-resistance versus co-resistance; human-to-pet transmission of AMR; seasonal and anthropogenic drivers of AMR; alternative interventions, including bacteriophages; and socio-behavioral determinants influencing antimicrobial misuse. This report summarizes the scientific deliberations and emerging research priorities identified during the meeting and highlights the urgent need for integrated, collaborative AMR surveillance across sectors and geographical regions, beginning with strengthened partnerships between India and the United Kingdom.

Oral administration of omega-3 polyunsaturated fatty acids (PUFAs) to rodents and humans is associated with an increase in gut bacteria that are predicted to synthesise short-chain fatty acids (SCFAs). We tested the hypothesis that physiological levels of omega-3 PUFAs in the distal intestinal lumen (1-50 μg/mL) are associated with increased SCFA synthesis in an in vitro fermentation model using faecal slurry from 10 healthy participants (mean age 30 years), with and without exogenous dietary fibres. SCFAs were measured by gas chromatography-flame ionisation detection (n = 10), and changes in bacterial composition were analysed by shotgun metagenomic sequencing (n = 6). In the presence of omega-3 PUFAs, there was a mean 9.3% (no inulin; P = 0.03) and 19.3% (+ 0.01 mg/mL inulin; P = 0.01) increase in total SCFA concentration at 24 h compared with paired control fermentations. Omega-3 PUFAs had a limited effect on the fermentation model microbiome in the absence of inulin. However, omega-3 PUFAs (50 μg/mL) were associated with increased abundance of Bifidobacteriaceae compared with paired control fermentations, if inulin (0.01 mg/mL) was present. Prebiotic activity of omega-3 PUFAs drives SCFA synthesis in an in vitro colonic fermentation model and is augmented by the soluble fibre inulin.

BACKGROUND:While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions. OBJECTIVE:To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia. DESIGN:Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates. RESULTS:Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R2=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone). CONCLUSION:This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.

Massively parallel sequencing technologies have been a boon to many fields of biological science, including oncology. Cancer is an umbrella term for many diseases featuring abnormal cellular growth due to genetic and epigenetic aberrations. Advances in sequencing technology allow for interrogation of the DNA and RNA of cancer cells and other cells in the tumor microenvironment down to a single-base resolution. However, these strides come after a rich history of ground-breaking biological assays, like the discovery of the Philadelphia chromosome in the context of leukemia. Many specific genetic and epigenetic modifications have been implicated in oncogenesis, cancer progression, and response to treatment. Sequencing technologies have also helped to associate populations of bacteria in the microbiome to cancer development and prognosis. However, all this new information, especially when procured via high-throughput methods, comes at the cost of being more computationally and staff-resource intensive. There is also more risk to the privacy of the individuals with sequenced genomes. Notwithstanding, the overall benefit of sequencing technologies can greatly outweigh the risks with careful advancements and continued focus on the goal: helping those affected by cancer via precision medicine. Cancer biology has been and will continue to be elucidated by sequencing innovations in ways unimaginable without it.

Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain understudied. Using samples from insects, reptiles, birds, and mammals, we integrated taxonomic, genomic, and predicted functional annotations to uncover how Bifidobacterium adapts to host-specific environments. Host phylogeny is a major determinant of gut microbial composition. Distinct microbiota in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, Bifidobacterium and their hosts exhibit strong co-phylogenetic associations, driven by vertical transmission and dietary selection. Functional analyses highlight striking host-specific adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, Bifidobacterium strains are enriched in glycoside hydrolases tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 α-amylases associated with degradation of resistant starch. Together, these findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.

BACKGROUND:The human gut microbiome is of academic and clinical interest. Associations between certain organisms and colorectal neoplasia have been reported, but findings have limited reproducibility in different populations. METHODS:We performed a systematic review of whole metagenome shotgun sequencing studies using faecal samples from patients with colorectal neoplasia and control populations. Searches were performed on 30th June 2023. We identified 26 studies, reporting on 22 study populations (13 from Asia, five from Europe and four from North America). Study size ranged from 14 to 971 individuals (mean 170). RESULTS:Some reproducible data were identified, such as the significant enrichment of Fusobacterium nucleatum and Parvimonas micra in colorectal cancer patients compared to controls (in 10 and nine studies, respectively). However, 21 out of 26 studies scored poorly on quality appraisal, specifically surrounding selection of cases and controls. Definitions of controls varied; some studies used individuals with normal endoscopic investigations, some used 'healthy' individuals where no colonoscopy was performed, and one used those with non-neoplastic findings (haemorrhoids). There was even less reproducibility of data in studies where individuals with colorectal polyps were compared to controls, possibly because of heterogeneity in these patient groupings as a variety of definitions for 'polyp cases' were used. CONCLUSIONS:Heterogeneity and potential for bias indicates that findings should be interpreted with caution. Standardised protocols to ensure robust methodology and allow pooling of large-scale data are required before these findings can be used in clinical practice (PROSPERO: CRD42023431977).

The Sundarban mangroves form a unique and productive ecosystem, essential for biodiversity conservation and ecological health, yet the role of archaeal communities in rhizosphere and their resilience under environmental stress remains poorly understood. This study aimed to investigate the archaeal community composition and functional potential in the rhizosphere soils of Avicennia officinalis and Ceriops decandra across Godkhali and Kalash, two ecologically distinct sites in the Indian Sundarban. Amplicon sequencing of the 16S rRNA gene revealed dominance of Crenarchaeota, Bathyarchaeia, and unclassified archaeal taxa, while halophilic lineages showed no plant-specific enrichment. Alpha diversity indices indicated similar richness and evenness across mangrove plant species and sites. Beta diversity and multivariate analyses demonstrated that community composition was shaped more by environmental factors, especially pollutant levels, than by plant species. Notably, ammonia-oxidizing archaea (AOA), including Nitrososphaera and Nitrosarchaeum, correlated positively with nitrogen concentrations, whereas methanogens and halophiles were associated with low oxygen and metal stress. DGGE profiling of archaeal amoA genes confirmed the widespread presence of AOA. Functional predictions via PICRUSt2 suggested enrichment of genes involved in metal resistance and hydrocarbon degradation. These findings highlight the adaptive role of archaeal communities in supporting rhizosphere resilience under environmental stress, contributing to ecosystem stability in the Sundarban.

Communicating key finds is a crucial part of the research process. Data visualization is the field of graphically representing data to help communicate key findings. Building on previous chapters around data manipulating using the R programming language this, chapter will explore how to use R to plot data and generate high-quality graphics. It will cover plotting using the base R plotting functionality and introduce the famous ggplot2 package [2] that is widely used for data visualization in R. After this general introduction to data visualization tools, the chapter will explore more specific data visualization techniques for metagenomics data and their use cases using these basic packages.

Background and Aims: Necrotizing enterocolitis (NEC) is a life-threatening disease and the most common gastrointestinal emergency in premature infants. Accurate early diagnosis is challenging. Modified Bell’s staging is routinely used to guide diagnosis, but early diagnostic signs are nonspecific, potentially leading to unobserved disease progression, which is problematic given the often rapid deterioration observed. We investigated fecal cytokine levels, coupled with gut microbiota profiles, as a noninvasive method to discover specific NEC-associated signatures that can be applied as potential diagnostic markers. Methods: Premature babies born below 32 weeks of gestation were admitted to the 2-site neonatal intensive care unit (NICU) of Imperial College hospitals (St. Mary’s or Queen Charlotte’s & Chelsea) between January 2011 and December 2012. During the NICU stay, expert neonatologists grouped individuals by modified Bell’s staging (healthy, NEC1, NEC2/3) and fecal samples from diapers were collected consecutively. Microbiota profiles were assessed by 16S rRNA gene amplicon sequencing and cytokine concentrations were measured by V-Plex multiplex assays. Results: Early evaluation of microbiota profiles revealed only minor differences. However, at later time points, significant changes in microbiota composition were observed for Bacillota (adj. P = .0396), with Enterococcus being the least abundant in Bell stage 2/3 NEC. Evaluation of fecal cytokine levels revealed significantly higher concentrations of IL-1α (P = .045), IL-5 (P = .0074), and IL-10 (P = .032) in Bell stage 1 NEC compared to healthy individuals. Conclusion: Differences in certain fecal cytokine profiles in patients with NEC indicate their potential use as diagnostic biomarkers to facilitate earlier diagnosis. Additionally, associations between microbial and cytokine profiles contribute to improving knowledge about NEC pathogenesis.

Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.

Microbial taxonomic assignment based on 16S marker gene amplification requires multiple data transformations, often encompassing the use of a variety of computational platforms. Bioinformatics analysis may represent a bottleneck for researchers as many tools require programmatic access in order to implement the software. Here we describe a step-by-step approach for taxonomic assignment using QIIME2 and highlight the utility of graphical-based microbiome tools for further analysis and identification of biological relevant taxa with reference to an outcome of interest.

The COLO‐COHORT study aims to produce a multi‐factorial risk prediction model for colorectal neoplasia that can be used to target colonoscopy to those at greatest risk of colorectal neoplasia, ensuring that people are not investigated unnecessarily and maximizing the use of limited endoscopy resources. The study will also explore the link between neoplasia and the human gut microbiome. Additionally, the study aims to generate a cohort of colonoscopy patients who are ‘research ready’ through the development of a consent‐for‐contact (C4C) platform, to facilitate a range of colorectal cancer prevention studies to be conducted at scale and speed.

The COLO-COHORT study aims to produce a multi-factorial risk prediction model for colorectal neoplasia that can be used to target colonoscopy to those at greatest risk of colorectal neoplasia, ensuring that people are not investigated unnecessarily and maximizing the use of limited endoscopy resources. The study will also explore the link between neoplasia and the human gut microbiome. Additionally, the study aims to generate a cohort of colonoscopy patients who are ‘research ready’ through the development of a consent-for-contact (C4C) platform, to facilitate a range of colorectal cancer prevention studies to be conducted at scale and speed. This is a multi-centre observational study involving sites across the UK. Recruitment is over a 6-year period (2019–2025). Patients recruited to the study are those attending for colonoscopy. Patients are recruited into two groups, namely observational group A (10 000 patients) and C4C group B (10 000 patients), known as COLO-SPEED (Colorectal Cancer Screening Prevention Endoscopy and Early Diagnosis; https://colospeed.uk ). Patients complete a health questionnaire, provide anthropometric measurements and submit biosamples (blood and stool—depending on the part of the study they are recruited into). Patients' colonoscopy and histology findings are also recorded. Models of factors associated with the presence of neoplasia at colonoscopy will be developed using logistic or multinomial regression. For internal validation, model discrimination and calibration will be assessed and bootstrapping and cross-validation approaches used. To enable long-term follow-up for outcomes related to colorectal cancer and polyps, patients are asked to consent to follow-up through data linkage with national databases. In keeping with good research practice, following analysis by the study team the study investigators will make the anonymized dataset available to other researchers. The C4C platform will also be accessible to other researchers. The study findings will be submitted for publication in peer-reviewed journals and lay summaries will be disseminated to participants and the wider public.

Objectives Necrotizing enterocolitis (NEC) is a life-threatening disease, and the most common gastrointestinal emergency in premature infants. Accurate early diagnosis is challenging. Modified Bell’s staging is routinely used to guide diagnosis, but early diagnostic signs are non-specific, potentially leading to unobserved disease progression, which is problematic given the often rapid deterioration observed in NEC infants. New techniques, using biomarkers as diagnostic tool to improve diagnosis of NEC, are emerging. Here we investigated faecal cytokine levels, coupled with gut microbiota profiles, as a non-invasive method to discover specific NEC-associated signatures that can be applied as potential diagnostic markers. Study design Premature babies born below 32 weeks of gestation were admitted to the 2-site neonatal intensive care unit (NICU) of Imperial College hospitals (St. Mary’s or Queen Charlotte’s & Chelsea) between January 2011 and December 2012. All but two babies received a first course of antibiotics from birth onwards. Faecal samples from diapers were collected consecutively during the NICU stay. Results Evaluation of microbiota profiles between the study groups revealed only minor differences. However, at later time points, significant changes in microbiota structure were observed for Firmicutes, with Enterococcus being the least abundant in Bell stage 2/3 NEC. Faecal cytokine levels were similar to those found in previous studies evaluating systemic cytokine concentrations in NEC settings, but measurement in faeces represents a non-invasive method to evaluate the early onset of the disease. For IL-1α, IL-5 and IL-10, a significantly rising gradient of levels were observed from healthy to NEC1 to NEC2/3. Conclusions Differences in certain faecal cytokine profiles in patients with NEC indicate their potential use as diagnostic biomarkers to facilitate earlier diagnosis. Additionally, associations between microbial and cytokine profiles, contribute to improving knowledge about NEC pathogenesis. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement LJH is supported by Wellcome Trust Investigator Awards (100974/C/13/Z and 220876/Z/20/Z); the Biotechnology and Biological Sciences Research Council (BBSRC), Institute Strategic Programme Gut Microbes and Health (BB/R012490/1), and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. Work at Imperial College was supported by a programme grant from the Winnicott Foundation to JSK, and the National Institute for Health Research (NIHR) Biomedical Research Centre based at Imperial Healthcare NHS Trust and Imperial College London. KS was funded by an NIHR Doctoral Research Fellowship [NIHR-DRF-2011-04-128]. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This work is part of the study Defining the Intestinal Microbiota in Premature Infants (NeoM The Neonatal Microbiota study) (ClinicalTrials.gov Identifier [NCT01102738][1]), approved by West London Research Ethics Committee Two, United Kingdom (Reference number: 10/H0711/39). Parents gave written approval for their infants to participate in the study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data availability: 16S rRNA gene amplicon data is available under BioProject accession number PRJNA889687. Cytokine data is provided in Supplementary Table 1. * NEC : Necrotizing enterocolitis NICU : neonatal intensive care unit VLBW : very low birthweight DOL : day of life OTU : operational taxonomic unit [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01102738&atom=%2Fmedrxiv%2Fearly%2F2022%2F10%2F26%2F2022.10.24.22281217.atom

Within the human intestinal tract, dietary, microbial- and host-derived compounds are used as signals by many pathogenic organisms, including Clostridioides difficile . Trehalose has been reported to enhance virulence of certain C. difficile ribotypes; however, such variants are widespread and not correlated with clinical outcomes for patients suffering from C. difficile infection (CDI). Here, we make preliminary observations on how trehalose supplementation affects the microbiota in an in vitro model and show that trehalose-induced changes can reduce the outgrowth of C. difficile , preventing simulated CDI. Three clinically reflective human gut models simulated the effects of sugar (trehalose or glucose) or saline ingestion on the microbiota. Models were instilled with sugar or saline and further exposed to C. difficile spores. The recovery of the microbiota following antibiotic treatment and CDI induction was monitored in each model. The human microbiota remodelled to utilise the bioavailable trehalose. Clindamycin induction caused simulated CDI in models supplemented with either glucose or saline; however, trehalose supplementation did not result in CDI, although limited spore germination did occur. The absence of CDI in trehalose model was associated with enhanced abundances of Finegoldia , Faecalibacterium and Oscillospira , and reduced abundances of Klebsiella and Clostridium spp., compared with the other models. Functional analysis of the microbiota in the trehalose model revealed differences in the metabolic pathways, such as amino acid metabolism, which could be attributed to prevention of CDI. Our data show that trehalose supplementation remodelled the microbiota, which prevented simulated CDI, potentially due to enhanced recovery of nutritionally competitive microbiota against C. difficile .