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Search for other papers by Andrija Karačić in
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Objective
The carnivore diet is a ketogenic diet based exclusively on the consumption of food of animal origin. While the impact of various diets on the gut microbiome is extensively documented, the effects of a carnivore diet remain unclear. To address this gap, we conducted a pilot study on the gut microbiome of an individual following a carnivore diet and compared it with that of a subgroup of healthy individuals.
Methods
A stool sample was collected from a healthy 32-year-old male adhering to a carnivore diet and was sequenced using 16S DNA Amplicon Sequencing. The results were then compared to those from three control groups possessing similar anthropometric characteristics and differing in their frequency of meat consumption.
Results
The gut microbiome of the carnivore was dominated by the phylum Firmicutes and the genera Faecalibacterium, Blautia, unspecific Lachnospiraceae, Bacteroides, and Roseburia—bacteria known for fiber degradation. Furthermore, neither alpha- nor beta-diversity, nor the functional capacity of the gut microbiome, showed differences when compared to the control groups. Additionally, the gut microbiome of the carnivore showed the least similarities with the microbiome of the cohort consuming meat on a daily basis.
Conclusions
In our study, we showcase the compositional and functional characteristics of the gut microbiome in an individual on a carnivorous diet, finding no differences in comparison to a control cohort. Further research is needed to investigate the short- and long-term impacts of a carnivorous diet on gut health through cross-sectional and longitudinal studies.
Significance statement
To the best of our knowledge this is the first study to report on the composition of the gut microbiome of a person adhering long-term to the carnivore diet.
Search for other papers by Claudio Costantini in
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Search for other papers by Mirco Dindo in
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Search for other papers by Marilena Pariano in
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Search for other papers by Claudia Stincardini in
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Search for other papers by Barbara Cellini in
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University San Raffaele and Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele, Rome, Italy
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Search for other papers by Kaushik Karambelkar in
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Systems and Control Engineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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Graphical abstract
Abstract
Objective
Preterm birth (PTB) is one of the leading issues concerning infant health and is a problem that plagues all parts of the world. Vaginal microbial communities have recently garnered attention in the context of PTB; however, the vaginal microbiome varies greatly from individual to individual, and this variation is more pronounced in racially, ethnically, and geographically diverse populations. Additionally, microbial communities have been reported to evolve during the duration of the pregnancy, and capturing such a signature may require higher, more complex modeling paradigms. In this study, we develop a neural controlled differential equation (CDE)-based framework for identifying early PTBs in racially diverse cohorts from irregularly sampled vaginal microbial abundance data.
Methods
We obtained relative abundances of microbial species within vaginal microbiota using 16S rRNA sequences obtained from vaginal swabs at various stages of pregnancy. We employed a recently introduced deep learning paradigm known as ‘neural CDEs’ to predict PTBs. This method, previously unexplored, analyzes irregularly sampled microbial abundance profiles in a time-series format.
Results
Our framework is able to identify signatures in the temporally evolving vaginal microbiome during trimester 2 and can predict incidences of PTB (mean test set ROC–AUC = 0.81, accuracy = 0.75, F1 score = 0.71) significantly better than traditional ML classifiers, thus enabling effective early-stage PTB risk assessment.
Conclusion and significance
Our method is able to differentiate between term and preterm outcomes with a substantial accuracy, despite being trained using irregularly sampled microbial abundance profiles, thus overcoming the limitations of traditional time-series modeling methods.
Search for other papers by Sweta Ghosh in
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Search for other papers by Venkatakrishna Rao Jala in
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Exposure to environmental pollutants such as heavy metals lead to significant damage in intestinal epithelial barrier, loss of microbial and immune homeostasis. The intestinal epithelial barrier protects and regulates the responses against several endogenous and exogenous factors including inflammatory cytokines, pathogens, toxins, and pollutants. Intestinal epithelial barrier dysfunction, immune dysregulation and microbial dysbiosis are associated with several gastrointestinal (GI)-related disorders including inflammatory bowel disease (IBD). The mechanisms and consequences of exposure to environmental toxins on gut barrier function and mucosal immune system are not fully understood. This review explores some of the recent findings of heavy metals and their effect on intestinal barrier function, microbiota, and their contributions to human health and pathogenesis of GI-related disorders such as IBD.
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German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
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The commensal microbiota resides in a mutualistic relationship within the mammalian gut. It significantly influences the formation of capillary networks in the small intestine, not only during development but also in adulthood. Mucosal capillaries in small intestinal villus structures play a critical role for the uptake of dietary nutrients and immune regulation. Emerging studies have elucidated how the composition of gut microbiota can influence not only postnatal gut development regarding immune tolerance, nutrient absorption, and morphology but also the development and maintenance of blood and lymphatic capillaries within the small intestine. In particular, the analysis of gnotobiotic mouse models affirmed the importance of the gut microbiota, or even only single gut bacteria, in the remodeling of the small intestinal capillaries. Here, different epithelial-to-endothelial cross talk pathways, e.g. Paneth cell-derived signals, Toll-like receptor signaling, or tissue factor–protease activated receptor-1 signaling, have been reported to affect intestinal villus vascular remodeling in a microbiota-dependent fashion. In this review article, we will provide a comprehensive overview on the relevant microbiota–host interaction pathways, which have been revealed to influence angiogenesis and vascular remodeling in the small intestine.
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Arome Science Inc., Farmington, Connecticut, USA
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Arome Science Inc., Farmington, Connecticut, USA
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Artificial intelligence (AI) is rapidly revolutionizing our daily lives, as it automates mundane tasks, enhances productivity, and transforms how we interact with technology. We believe it is inevitable that AI will soon become a crucial tool in common research practices, from data analysis to writing papers. Here we explore how this transition is occurring in the field of mass spectrometry-based metabolomics, a rapidly growing area of science. Metabolomics focuses on studying small molecules in biological systems, offering valuable insights into metabolic processes and their impact on health, diseases, and physiological conditions. With the remarkable advancements in sequencing technologies and the exploration of the microbiome, the combination of sequencing and metabolomics presents profound opportunities to understand biological complexity. Incorporating AI is promising to unlock new possibilities for expanding the realms of scientific discoveries. In this review we specifically focus on the current trends in the application of AI in metabolomics research. Existing practices are examined and a perspective on future directions for integrating AI into metabolomics research is presented.
Department of Animal Care Science, Smithsonian National Zoo and Conservation Biology Institute, Front Royal, Virginia, USA
Department of Biological Sciences, College of Sciences, North Carolina State University, Raleigh, North Carolina, USA
Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Objective
Gut health and its relationship to gut microbiota is an important consideration in the care and well-being of managed endangered species, such as the cheetah (Acinonyx jubatus). Non-invasive fecal sampling as a proxy for gut microbiota is preferred and collecting fresh fecal samples is the current gold standard. Unfortunately, even in managed facilities, collecting fresh samples from difficult to observe or dangerous animals is challenging. Therefore, we conducted a study to determine the terminal collection timepoint for fecal microbial studies in the cheetah.
Methods
We longitudinally sampled eight freshly deposited fecals every 24 h for 5 days and assessed bacterial relative abundance, diversity, and composition changes over time.
Results
Our data indicated that fecal samples up to 24 h post defecation provided accurate representations of the fresh fecal microbiome. After 24 h, major changes in community composition began to occur. By 72 h, individual cheetah fecal microbiota signatures were lost.
Conclusion
Our findings suggest that cheetah fecal samples should be collected within 24 h of defecation in humid environments, especially if precipitation occurs, in order to provide a more biologically accurate representation of the gut microbiome, and we provide visual characteristics that can aid researchers in approximating time since defecation.
Significance statement
Data from this study provides guidelines for researchers investigating cheetah and other large felids and carnivores where the ability to collect fresh fecal deposits is limited.
Healthy Landscapes Research Group, University of Tasmania, Sandy Bay, Tasmania, Australia
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Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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Future in Nature Pty Ltd, Australia
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Healthy Landscapes Research Group, University of Tasmania, Sandy Bay, Tasmania, Australia
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This systematic review aims to investigate how urban living influences the microbiome of wildlife. We included all studies that compared the bacterial communities of non-human vertebrate wildlife living inside vs outside cities, and/or across an urbanisation gradient. We found that the effect of urban living on bacterial diversity and community composition was not unidirectional: some studies found a positive association, others found a negative association, and some found no relationship. The definition of ‘urban’ was not specified in more than half of the studies, and when included, was not consistent across studies; paired with limited site replication in many studies, these features could have obscured the impacts of urban living. Most studies also focused on urban-adapted wildlife species. Future studies that include clear definitions for ‘urban’ environments and good replication of land uses within contrasting environments would help clarify the impact of urban living on wildlife microbiomes and wildlife health.
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Objective
This study aims to evaluate the impact of cesarean section delivery on the neonatal intestinal microflora compared to vaginal deliveries.
Design
A mini-review.
Methods
A comprehensive search strategy was implemented, primarily using PubMed, to identify relevant studies published in English within the past 10 years. Selected studies were appraised by three independent reviewers using JBI critical appraisal and data extraction forms. Four articles were included in the analysis, encompassing systematic reviews and a retrospective cohort study. Primary and secondary outcome data were combined across these studies.
Results
Selected studies revealed consistent trends in bacterial colonization differences between cesarean and vaginal deliveries. Vaginally delivered infants exhibited higher populations of beneficial bacteria such as Bifidobacterium, Lactobacillus, and Bacteroides. Cesarean-delivered infants, on the other hand, showed greater colonization of Enterococcus, Klebsiella, Clostridium, Staphylococcus, Streptococcus, and Corynebacterium. Statistically significant differences were observed in two studies. All articles explored the potential health implications of these microbiome differences, with associations found between cesarean deliveries and various health outcomes.
Conclusion
This review demonstrates that cesarean section delivery influences the composition of the neonatal gut microbiota. The presence of certain bacterial species more prevalent in vaginally delivered infants, such as Bifidobacterium, is associated with improved infant health, while species found in cesarean-delivered infants, such as Clostridium, increase the risk of certain infections. Recognizing the increased health risks for cesarean-born infants enables clinicians to implement early screening, treatment, or prevention strategies, potentially reducing future morbidity and mortality.
Department of Immunology, Mayo Clinic Rochester, Minnesota, USA
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Department of Pediatrics, Mayo Clinic Rochester, Minnesota, USA
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The health of the intestinal microbiota impacts tolerance at homeostasis and the strength of the inflammation response during acute bloodstream infections. A complete understanding of the feedback loop between systemic inflammation and dysregulation of the gut microbiota is necessary for inflammation management. Here we will review the many ways in which the microbiota can influence the systemic pro-inflammatory response. Short-chain fatty acids, produced through the microbial metabolism of dietary fibers, can suppress inflammation systemically; in the absence of a balanced diet or disruption of the microbiota through antibiotics, there is disrupted metabolite production, leading to systemic inflammation. Dysbiosis or inflammation in the intestines can lead to a breakdown of the sturdy intestinal–epithelial barrier. When this barrier is perturbed, immunogenic lipopolysaccharides or extracellular vesicles enter the bloodstream and induce excessive inflammation. Necessary clinical treatments, such as antifungals or antibacterials, induce microbiota dysregulation and thus increased risk of endotoxemia; though probiotics may aid in improving the microbiota health and have been shown to deflate inflammation during sepsis. Within this complicated relationship: What is in control, the dysbiotic microbiota or the systemic inflammation?
