Biology subjects

Caim, S.

Publications and source records attributed to Caim, S..

14 recordsLinked to original sources

bioRxiv2024

Early life milk diets shape infant gut microbiota: evidence of microbial plasticity in response to breast and formula milk.

In early life, diet plays a key role in shaping the infant microbiota, yet the impact of breast milk and formula on microbial ecosystems at different stages of infant development remains poorly understood. Here, we performed static batch culture experiments using infant faecal samples at ages 1, 12 and 18 months of age, supplemented with either breast milk or formula for 48 hours. We further removed small metabolites (e.g. small carbohydrates, proteins and lipids) from breast and formula milk through dialysis and also added this to the static batch cultures with faecal samples from each infant. Our results show that the one-month-old faecal microbiota exhibited the greatest sensitivity to dietary intervention, with significant changes in microbial composition, metabolites and lipids, particularly in response to formula supplementation. In contrast, the microbiota at 12 months displayed increased stability, while the 18-month-old infant samples were the most resilient to different dietary supplementation. We also observed that triglyceride (TG46:1) was produced in the youngest infant samples but consumed by the older infant microbiota, suggesting a shift in metabolic interactions as the gut microbiota diversifies with age. Metabolite profiles linked to KEGG pathways further indicated the older infants diverse microbiotas had greater functional capacity in comparison to the one-month-old infant, particularly in response to breast milk. Fewer overall metabolic pathways were affected when the infant samples were grown in formula. Collectively, our data underscores the importance of early life diet in shaping microbiota profiles, with more stable microbial dynamics in more mature gut ecosystems, in response to dietary changes which are also associated with downstream functional (i.e. metabolite/lipid) readouts. Notably, the removal of small metabolites from breast milk by dialysis highlighted the potential role of milk lipids in promoting growth of foundational microbiota members like Bifidobacterium. Our data, along with further studies, are required to probe the mechanisms by which specific nutrients, particularly lipids, modulate microbial composition and support infant health during the first 2 years of life.

microbiology↗

bioRxiv2023

Gut microbiota and faecal cytokine profiles of rural Cambodian infants and links to early life nutrition and diarrhoeal episodes.

The gut microbiota of infants in low-middle income countries like Cambodia remain underrepresented in microbiome research. This study aimed to explore the faecal gut microbiota composition and faecal cytokine profiles in a cohort of infants living in a rural province of Cambodia and explore the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants (96 samples in total) after 7 months of age were analysed using 16S rRNA amplicon sequencing to determine the composition of the microbiota. Bacterial strains were isolated and subjected to whole genome sequencing and genomic analysis and concentrations of faecal cytokines were also measured. Initially, we compared the effects of two sample collection methods due to the challenges of faecal sample collection and storage in a rural location. Storage of faecal samples in a DNA preservation solution retained a greater abundance of Bacteroides. Analyses of microbiota composition of samples stored in DNA preservation solution indicated that Bifidobacterium was the most abundant genus with Bifidobacterium longum the most abundant species, particularly in breastfed infants. Most infants had detectable pathogenic taxa indicating frequent pathogen exposure, with Shigella and Klebsiella more abundant in infants with recent diarrheal illness. We did not detect antibiotic-associated perturbations in the gut microbiota, and no associations were found between the gut microbiota and infant growth. Genomic analysis of isolated strains indicated the presence of gene clusters encoding the ability to digest human milk oligosaccharides in B. longum and Bifidobacterium breve isolates. The presence of antibiotic-resistant genes was also identified in potentially pathogenic species, as well as in beneficial genera including Bifidobacterium. Faecal cytokine analysis showed higher concentrations of Interlukin-1alpha and vascular endothelial growth factor in breastfed infants, which may influence the infant gut mucosal immune system. This study provides insights into an underrepresented population of rural Cambodian infants, emphasising the impact of pathogen exposure and breastfeeding on gut microbiota composition and faecal immune profiles.

microbiology↗

bioRxiv2020

Bifidobacterium breve UCC2003 induces a distinct global transcriptomic programme in neonatal murine intestinal epithelial cells

Bifidobacterium is an important gut microbiota member during early life that is associated with improved gut health. However, the underlying health-driving mechanisms are not well understood, particularly how Bifidobacterium may modulate the intestinal barrier via programming of intestinal epithelial cells (IECs). In this study, we sought to investigate the global impact of model strain Bifidobacterium breve UCC2003 on the neonatal IEC transcriptome, including gene regulation and pathway modulation. Small IECs from two-week-old neonatal mice administered B. breve UCC2003 for three consecutive days or PBS (control group) were subjected to global RNASeq, with various bioinformatic approaches used to determine differentially expressed genes, pathways and affected cell types between control and experimental groups. Whilst colonisation with B. breve had minimal impacts on the neonatal microbiota, we observed extensive regulation of the IEC transcriptome; ~4,000 genes significantly up-regulated, including key genes associated with epithelial barrier function. Enrichment of cell differentiation and cell proliferation pathways were observed, along with an overrepresentation of stem cell marker genes, indicating an increase in the regenerative potential of the epithelial layer. Expression of distinct immune-associated pathway members (e.g. Toll-like Receptors) were also affected after neonatal B. breve colonisation. In conclusion, B. breve UCC2003 plays a central role in driving universal transcriptomic changes in neonatal IECs that enhances cell replication, differentiation and growth, predominantly in the stem cell compartment. This study enhances our overall understanding of the benefits of B. breve in driving intestinal epithelium homeostatic development during early life, with potential avenues to develop novel live biotherapeutic products.

immunology↗

bioRxiv2020

Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumour growth via a mast cell-dependent pathway

The diverse community of commensal microbes that comprise the gut microbiota is known to play an integral role in human health, not least through its ability to regulate host immune responses and metabolic pathways. Alterations to the homeostasis of this community, including through the use of broad-spectrum antibiotics, have already been associated with the progression of several cancers, namely melanoma and liver. The aggressive nature of breast cancer (BrCa), largely due to its ability to metastasize early, has ranked the disease with the second highest mortality rate of all cancers globally. Yet the body of research into the complex relationship between the microbiota and BrCa is still limited. This study found that a depletion of the microbiota, through the administration of antibiotics, significantly increased the rate of primary tumour progression in mouse BrCa models. We show that antibiotic-induced microbiota disturbances lead to changes in behaviour of a relatively obscure tumour-immune cell population: mast cells. We observed increases in tumour stroma-associated mast cells in antibiotic treated animals. Moreover, inhibition of mast cell degranulation, via cromolyn, slowed tumour progression in antibiotic treated animals but not in control animals. Thus, it appears that a perturbed microbiota drives stroma-associated mast cell recruitment and activation, which in turn promotes primary tumour growth through an as yet unknown mechanism. One Sentence Summary: We show that breast cancer progression is accelerated through a unique/novel immune response involving mast cells as a result of an antibiotic induced perturbation of the gut microbiota in a mouse model.

cancer biology↗

bioRxiv2019

Bifidobacterium breve UCC2003 exopolysaccharide modulates the early life microbiota by acting as a dietary substrate

Members of the genus Bifidobacterium represent an important bacterial group for promoting health during early life. Previous studies have indicated that bifidobacterial exopolysaccharides (EPS) are involved in host interactions, with purified EPS also suggested to modulate microbe-microbe interactions by acting as a nutrient substrate. To further explore the role of EPS as a potential dietary component, we determined the longitudinal effects of bifidobacterial EPS on microbial communities and metabolite profiles using an infant model colon system. Bifidobacterium breve UCC2003 was utilised as a representative early life bifidobacterial strain, and a corresponding isogenic EPS-deletion mutant (B. breve UCC2003 EPS-). Initial transcriptomics analysis of the EPS mutant vs. parent B. breve UCC2003 strain highlighted differential expression in a discrete number of genes, including the eps biosynthetic cluster, though overall growth dynamics between the two strains were unaffected. Model colon vessels were inoculated with B. breve strains and microbiome dynamics were monitored using metataxonomic (via 16S rRNA sequencing) and metabolomic (via 1H NMR) approaches. Baseline early life microbiota profiles were similar between vessels, with persistence of B. breve (EPS+ and EPS-) observed between 0-36h. Within the EPS-positive vessel there was a significant shift in microbiome and metabolite profiles until the end of the study (405h); we observed increases of Escherichia and Tyzzerella, and short-chain fatty acids including acetate, propionate and formate, including further correlations between taxa and metabolites which were not observed in the EPS-negative vessel. These data indicate that the B. breve UCC2003 EPS is potentially being metabolised by members of the infant microbial community, leading to differential microbial metabolism and altered metabolite by-products. Overall, these findings may allow for development of EPS-specific strategies to beneficially alter the early life microbiota to promote infant health.

microbiology↗

bioRxiv2019

The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding

The gut microbiota plays a crucial role in regulating and maintaining the epithelial barrier, particularly during early life. Notably, patients with chronic intestinal inflammation have a dysregulated process of renewal and replenishment of the intestinal epithelial cell (IEC) barrier, which is linked to disturbances in the gut microbiota. To date, there are no studies focussed on understanding the impact of inflammatory cell shedding events during the early life developmental window, and which host and microbial factors mediate these responses. Here we sought to determine pathological cell shedding outcomes throughout the postnatal developmental period (day 14, 21, 29 and week 8). Surprisingly neonatal mice (day 14 and 21) were highly refractory to induction of cell shedding after intraperitoneal administration of LPS, with day 29 mice showing strong pathological responses, more similar to those observed in adult mice. These differential responses were not linked to defects in the cellular mechanisms and pathways known to regulate cell shedding responses, although we did observe that neonatal mice had elevated anti-inflammatory (IL-10) responses. Notably, when we profiled microbiota and metabolites from these mice, we observed significant alterations. Neonatal mice had high relative abundances of Streptococcus, Escherichia and Enterococcus and increased primary bile acids. In contrast, older mice were dominated by Candidatus Arthromitus, Alistipes and Lachnoclostridium, and had increased concentrations of SCFAs and methyamines. Faecal microbiota transplant (FMT) and antibiotic studies confirmed the importance of early life gut microbiota in cell shedding responses. In these studies, neonates treated with antibiotics restored LPS-induced small intestinal cell shedding, whereas adult FMT alone had no effect. Our findings further support the importance of the early life window for microbiota-epithelial interactions in the presence of inflammatory stimuli and highlight areas for further investigation to probe underlying mechanisms to drive therapeutic development within the context of chronic inflammatory intestinal diseases.

microbiology↗

bioRxiv2019

Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors

Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis, nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella as previous studies have focussed on recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for isolates. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. healthy) encoded multiple {beta}-lactamases, which may prove problematic when defining treatment regimens for NEC or sepsis, and suggest healthy preterm infants contribute to the resistome. No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Using a curated dataset of Klebsiella oxytoca, K. grimontii and K. michiganensis whole-genome sequences, metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut, and highlight the importance of refined analyses with curated sequence databases when studying closely related species present in metagenomic data.

microbiology↗

bioRxiv2019

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome

Supplementation with members of the early-life microbiota or probiotics is becoming increasingly popular to attempt to beneficially manipulate the preterm gut microbiota. We performed a large longitudinal study comprising two preterm groups; 101 orally supplemented with Bifidobacterium and Lactobacillus (Bif/Lacto) and 133 non-supplemented (Control) matched by age, sex, birth-mode, and diet. 16S rRNA metataxonomic profiling on stool samples (n = 592) indicated a predominance of Bifidobacterium, and a reduction of pathobionts in the Bif/Lacto group. Metabolic phenotyping found a parallel increase in fecal acetate and lactate in the Bif/Lacto group compared to the Control group, which positively correlated with Bifidobacterium abundance consistent with the ability of the supplemented Bifidobacterium strain to metabolize human milk oligosaccharides and reduced gut pH. This study demonstrates that microbiota supplementation can modify the preterm microbiome and the gastrointestinal environment to more closely resemble that of a full-term infant.

microbiology↗

bioRxiv2019

Genomic analysis on broiler-associated Clostridium perfringens strains and caecal microbiome profiling reveals key factors linked to poultry Necrotic Enteritis

BackgroundClostridium perfringens is a key pathogen in poultry-associated necrotic enteritis (NE). To date there are limited Whole Genome Sequencing based studies describing broiler-associated C. perfringens in healthy and diseased birds. Moreover, changes in the caecal microbiome during NE is currently not well characterised. Thus, the aim of this present study was to investigate C. perfringens virulence factors linked to health and diseased chickens, including identifying caecal microbiota signatures associated with NE.\n\nResultsWe analysed 88 broiler chicken C. perfringens genomes (representing 66 publicly available genomes and 22 newly sequenced genomes) using different phylogenomics approaches and identified a potential hypervirulent and globally-distributed clone spanning 20-year time-frame (1993-2013). These isolates harbored a greater number of virulence genes (including toxin and collagen adhesin genes) when compared to other isolates. Further genomic analysis indicated exclusive and overabundant presence of important NE-linked toxin genes including netB and tpeL in NE-associated broiler isolates. Secondary virulence genes including pfoA, cpb2, and collagen adhesin genes cna, cnaA and cnaD were also enriched in the NE-linked C. perfringens genomes. Moreover, an environmental isolate obtained from farm animal feeds was found to encode netB, suggesting potential reservoirs of NetB-positive C. perfringens strains (toxinotype G). We also analysed caecal samples from a sub-set of 11 diseased and healthy broilers using 16S rRNA amplicon sequencing, which indicated a significant and positive correlation in genus Clostridium within the wider microbiota of those broilers diagnosed with NE, alongside reductions in beneficial microbiota members.\n\nConclusionsThese data indicate a positive association of virulence genes including netB, pfoA, cpb2, tpeL and cna variants linked to NE-linked isolates. Potential global dissemination of specific hypervirulent lineage, coupled with distinctive microbiome profiles, highlights the need for further investigations, which will require a large worldwide sample collection from healthy and NE-associated birds.

microbiology↗

bioRxiv2019

Phylogenomic analysis of Clostridium perfringens identifies isogenic strains in gastroenteritis outbreaks, and novel virulence-related features

Clostridium perfringens is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, limited Whole Genome Sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of C. perfringens-associated outbreak strains. We performed both genomic and phylogenetic analysis on 109 C. perfringens strains (human and food) isolated from disease cases in England and Wales between 2011-2017. Initial findings highlighted the enhanced discriminatory power of WGS in profiling outbreak C. perfringens strains, when compared to the current Public Health England referencing laboratory technique of Fluorescent Amplified Fragment Length Polymorphism (fAFLP). Further analysis identified that isogenic C. perfringens strains were associated with nine distinct care home-associated outbreaks over the course of a 5-year interval, indicating a potential common source linked to these outbreaks or transmission over time and space. As expected the enterotoxin CPE gene was encoded in all but 4 isolates (96.4%; 105/109), with virulence plasmids encoding cpe (particularly pCPF5603- and pCPF4969-family plasmids) extensively distributed (82.6%;90/109). Genes encoding accessory virulence factors, such as beta-2 toxin, were commonly detected (46.7%; 50/109), and genes encoding phage proteins were also frequently identified, with additional analysis indicating their contribution to increased virulence determinants within the genomes of gastroenteritis-associated C. perfringens. Overall this large-scale genomic study of gastroenteritis-associated C. perfringens suggested that 3 major sub-types underlie these outbreaks: strains carrying (1) pCPF5603 plasmid, (2) pCPF4969 plasmid, and (3) strains carrying cpe on transposable element Tn5565(usually integrated into chromosome). Our findings indicate that further studies will be required to fully probe this enteric pathogen, particularly in relation to developing intervention and prevention strategies to reduce food poisoning disease burden in vulnerable patients, such as the elderly.

microbiology↗

bioRxiv2019

Perturbation of the gut microbiota by antibiotics results in accelerated breast tumour growth and metabolic dysregulation

BackgroundBreast cancer is the second most prevalent cancer worldwide with around 1.7 million new cases diagnosed every year. Whilst prognosis is generally favourable in early stages, this worsens significantly in advanced disease. Therefore, it is pertinent to focus on mitigating factors that may slow growth or progression. Recently, the gut microbiome has been implicated in a wide-range of roles in tumour biology. Through modulation of immunity, the gut microbiota can improve the efficacy of several immunotherapies. However, despite the prevalence of breast cancer, there is still a lack of microbiota studies in this field, including exploring the influence of external microbiome-modulating factors such as antibiotics. We describe herein how disruption of the gut microbiota via antibiotics may be detrimental to patient outcomes through acceleration of tumour growth. ResultsSupplementing animals with a cocktail of antibiotics leads to gut microbiota alterations and is accompanied by significant acceleration of tumour growth. Surprisingly, and distinct from previous microbiome-tumour studies, the mechanism driving these effects do not appear to be due to gross immunological changes. Analysis of intratumoural immune cell populations and cytokine production are not affected by antibiotic administration. Through global tumour transcriptomics, we have uncovered dysregulated gene expression networks relating to protein and lipid metabolism that are correlated with accelerated tumour growth. Fecal metabolomics revealed a reduction of the microbial-derived short-chain fatty acid butyrate that may contribute to accelerated tumour growth. Finally, through use of a routinely administered antibiotic in breast cancer patients, Cephalexin, we have shown that tumour growth is also significantly affected. Metataxanomic sequencing and analysis highlighted significant antibiotic-associated reductions in the butyrate producing genera Odoribacter and Anaeotruncus, and increased abundance of Bacteroides. ConclusionsOur data indicate that perturbation of the microbiota by antibiotics may have negative impacts on breast cancer patient outcomes. This is of importance as antibiotics are regularly prescribed to breast cancer patients undergoing mastectomy or breast reconstruction. We have also shown that the metabolic impact of disruption to the microbiome should be considered alongside the potent immunological effects. We believe our work lays the foundation for improving the use of antibiotics in patients, and with further investigation could potentially inform clinical practice.

cancer biology↗

bioRxiv2018

Streaming histogram sketching for rapid microbiome analytics

MotivationThe growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research; allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time.\n\nTo address this need, we propose a new method for the compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching, and classification of microbiome samples in near real-time.\n\nResultsWe apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed histosketch that can be used to efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we show that histosketches can be used to train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a Random Forest Classifier that could accurately predict whether the neonate had received antibiotic treatment (95% accuracy, precision 97%) and could subsequently be used to classify microbiome data streams in less than 12 seconds.\n\nWe provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2GB microbiome in 50 seconds on a standard laptop using 4 cores, with the sketch occupying 3000 bytes of disk space.\n\nAvailabilityOur implementation (HULK) is written in Go and is available at: https://github.com/will-rowe/hulk (MIT License)

genomics↗

bioRxiv2017

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

The performance of RNA-Seq aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Here we show that the accuracy of transcript reconstruction can be boosted by combining multiple methods, and we present a novel algorithm to integrate multiple RNA-Seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified metrics, while solving common artefacts such as erroneous transcript chimerisms. We have implemented this method in an open-source Python3 and Cython program, Mikado, available at https://github.com/lucventurini/Mikado.

bioinformatics↗

bioRxiv2017

Rapid MinION metagenomic profiling of the preterm infant gut microbiota to aid in pathogen diagnostics

The Oxford Nanopore MinION sequencing platform offers near real time analysis of DNA reads as they are generated, which makes the device attractive for in-field or clinical deployment, e.g. rapid diagnostics. We used the MinION platform for shotgun metagenomic sequencing and analysis of gut-associated microbial communities; firstly, we used a 20-species human microbiota mock community to demonstrate how Nanopore metagenomic sequence data can be reliably and rapidly classified. Secondly, we profiled faecal microbiomes from preterm infants at increased risk of necrotising enterocolitis and sepsis. In single patient time course, we captured the diversity of the immature gut microbiota and observed how its complexity changes over time in response to interventions, i.e. probiotic, antibiotics and episodes of suspected sepsis. Finally, we performed real-time runs from sample to analysis using faecal samples of critically ill infants and of healthy infants receiving probiotic supplementation. Real-time analysis was facilitated by our new NanoOK RT software package which analysed sequences as they were generated. We reliably identified potentially pathogenic taxa (i.e. Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance (AMR) gene profiles within as little as one hour of sequencing. Antibiotic treatment decisions may be rapidly modified in response to these AMR profiles, which we validated using pathogen isolation, whole genome sequencing and antibiotic susceptibility testing. Our results demonstrate that our pipeline can process clinical samples to a rich dataset able to inform tailored patient antimicrobial treatment in less than 5 hours.

genomics↗