Article
Genetics & Heredity
Taro Onuma, Toshitaka Yamauchi, Hina Kosakamoto, Hibiki P. Kadoguchi, Takayuki Kuraishi, Takumi P. Murakami, Hiroshi Mori, Masayuki P. Miura, Fumiaki Obata
Summary: Commensal microbes have a significant impact on tissue homeostasis, stress resistance, and ageing in animals. This study investigates the molecular mechanism behind how a specific gut bacterium shortens lifespan and promotes intestinal stem cell proliferation in fruit flies. The findings reveal that the bacterium induces the production of antimicrobial peptides and alters the balance between lifespan and host defence through peptidoglycan specificity.
Review
Microbiology
Michiel Van de Vliet, Marie Joossens
Summary: Understanding the initial colonization process of the human intestines is crucial for preventing microbiota-associated diseases and improving microbial therapies. Due to a lack of standardization, current insights are largely based on deduction and assumption. Comparing research in piglets, which have similar intestinal tracts to humans, it is found that the colonization process is similar and the bacterial community itself plays a major role in colonization success.
Article
Biotechnology & Applied Microbiology
Himani Khurana, Monika Sharma, Meghali Bharti, Durgesh Narain Singh, Ram Krishan Negi
Summary: Silver carp is an invasive fish in Gobindsagar reservoir, India, with profound impacts. Analysis of microbial composition in gut regions and water samples revealed distinct microbial communities and niche specialization in different gut regions. Proteobacteria was the most abundant phylum, and the gut microbiota specialized in digestive functions in different regions, reflecting the dietary profile of silver carp.
Article
Biology
Elizabeth R. Hughes, Maria G. Winter, Laice Alves da Silva, Matthew K. Muramatsu, Angel G. Jimenez, Caroline C. Gillis, Luisella Spiga, Rachael B. Chanin, Renato L. Santos, Wenhan Zhu, Sebastian E. Winter
Summary: During intestinal inflammation, the composition of gut-associated microbial communities changes, with an increase in Enterobacteriaceae populations. The analysis of microbial hydrogen metabolism revealed that bacterial genomes in the inflamed gut contained more genes encoding predicted hydrogen-utilizing hydrogenases. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed gut, suggesting the importance of hydrogenases in the context of non-infectious colitis.
Article
Cell Biology
Caijun Zhao, Lijuan Bao, Min Qiu, Keyi Wu, Yihong Zhao, Lianjun Feng, Kaihe Xiang, Naisheng Zhang, Xiaoyu Hu
Summary: This study found that cows with mastitis had significant gut dysbiosis, characterized by enrichment of opportunistic pathogenic bacteria and depletion of commensal bacteria. Fecal microbiota transplantation from cows with mastitis to mice induced mastitis and altered gut and mammary microbiota in mice. The commensal bacteria improved mastitis symptoms by producing butyrate, limiting bacterial translocation.
Article
Cell Biology
Jessica Spring, Aly A. Khan, Sophie Lara, Kelly O'Grady, Jessica Wilks, Sandeep Gurbuxani, Steven Erickson, Michael Fischbach, Amy Jacobson, Alexander Chervonsky, Tatyana Golovkina
Summary: The microbiota plays a significant role in retroviral pathogenesis by promoting leukemia development through suppression of the immune response. The upregulation of negative regulators of immunity by commensal bacteria suggests potential targets for cancer therapy.
Review
Biotechnology & Applied Microbiology
Gerald W. Tannock
Summary: The large bowel of monogastric animals, such as humans, is home to a diverse microbial community (microbiota) mainly composed of bacteria. The relationship between the microbiota and the host is complex and lifelong, characterized by symbiosis. Dysbiosis may occur as a result of disease, disrupting the relationship. Understanding the mechanisms by which symbionts inhabit the gut is crucial for correcting dysbiosis.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Shivohum Bahuguna, Magda Atilano, Marcus Glittenberg, Dohun Lee, Srishti Arora, Lihui Wang, Jun Zhou, Siamak P. Redhai, Michael P. Boutros, Petros P. Ligoxygakis
Summary: The immune system of fruit flies recognizes gut bacteria and activates a metabolic pathway to regulate lipid breakdown, which is important for the retention of intestinal bacteria. The TOR pathway inhibits lipid breakdown in fly mutants with reduced immune recognition, leading to increased gut fat accumulation. Blocking the TOR pathway restores both lipid levels and the density of gut bacteria to normal levels.
Article
Microbiology
E. E. Putnam, J. Abellon-Ruiz, B. J. Killinger, J. J. Rosnow, A. G. Wexler, E. Folta-Stogniew, A. T. Wright, B. van den Berg, A. L. Goodman
Summary: This study focuses on a new protein called BtuH in gut Bacteroidetes, which plays a key role in vitamin B-12 transport and competitive fitness in the gut. It suggests that accessory proteins encoded in Bacteroides cobamide transport system loci can have significant impacts on vitamin acquisition in the gut, demonstrating the complexity of the gut microbiome.
Article
Cell Biology
Lucille C. Rankin, Katherine A. Kaiser, Kenia de los Santos-Alexis, Heekuk Park, Anne-Catrin Uhlemann, Nicholas Arpaia, Daniel H. D. Gray
Summary: Micronutrient deficiency is a leading cause of global diseases. This study reveals that a deficiency in dietary tryptophan (Trp) alters the intestinal microbiome and the immune response, resulting in changes to the Treg cell population. Dietary Trp deficiency leads to the expansion of RORgt+ Treg cells and the loss of Gata3+ Tregs, which can be restored by providing the AhR ligand indole-3-carbinol. These findings emphasize the crucial role of immune-microbiome crosstalk in regulating Treg homeostasis during nutrient deficiency.
Article
Biochemistry & Molecular Biology
Arianna Mazzoli, Cristina Gatto, Raffaella Crescenzo, Maria Stefania Spagnuolo, Martina Nazzaro, Susanna Iossa, Luisa Cigliano
Summary: The study found that while temporarily discontinuing the consumption of a diet rich in fructose can fully restore liver function, these changes persist in the gut, especially in the ileum.
Article
Ecology
Shou-Ke Zhang, Yi Wang, Zi-Kun Li, Huai-Jun Xue, Xu-Dong Zhou, Jun-Hao Huang
Summary: The study suggests that the gut microbiome may play a role in the food niche competition of herbivorous insects, especially in the degradation of plant toxic compounds. Gut microbiomes with diverse microorganisms and enriched pathways for degrading plant toxins may contribute to the success of insects in food niche competition.
Article
Microbiology
Katie Lynn Summers, Juli Foster Frey, Ann M. Arfken
Summary: This study characterized the growth conditions, antifungal susceptibility, biofilm formation, and genetic relatedness of Kazachstania slooffiae. Results suggest potential symbiotic relationships with beneficial bacteria and positive effects on pig gut health.
Article
Microbiology
Caroline Tawk, Bentley Lim, Natasha A. Bencivenga-Barry, Hannah J. Lees, Ruben J. F. Ramos, Justin Cross, Andrew L. Goodman
Summary: Gastrointestinal infection can alter microbiome composition and gene expression. This study reveals that enteric infection also leads to rapid genetic adaptation in gut commensals. By studying Bacteroides thetaiotaomicron population dynamics in gnotobiotic mice, it was observed that the introduction of the enteropathogen Citrobacter rodentium promotes selection of a single-nucleotide variant with increased fitness. This variant mutation enhances resistance to oxidative stress by affecting the sequence of a fitness essential protein, IctA. Furthermore, it was found that certain commensal species can attenuate the selection of this variant during infection and this attenuation is associated with increased levels of vitamin B6 in the gut lumen. Direct administration of vitamin B6 significantly reduces variant expansion in infected mice, indicating its potential as a therapeutic target in enteric infections.
CELL HOST & MICROBE
(2023)
Article
Microbiology
Thaisa M. Cantu-Jungles, Nuseybe Bulut, Eponine Chambry, Andrea Ruthes, Marcello Iacomini, Ali Keshavarzian, Timothy A. Johnson, Bruce R. Hamaker
Summary: The study suggests that high-specificity dietary fibers result in more similar responses in gut microbiota, while low-specificity dietary fibers lead to different responses among subjects. High-specificity fibers can promote targeted and predictable microbial shifts in the gut.
Article
Genetics & Heredity
Sean M. Kearney, Elaina Thomas, Allison Coe, Sallie W. Chisholm
Summary: The composition of heterotrophs varied between different clades and ecotypes of autotrophic hosts, but there was significant overlap in heterotroph community composition across enrichment cultures. Factors such as time since isolation, location, depth, and isolation methods were associated with differences in community composition. While most heterotrophs in cultures are rare in the global ocean, some, like those in the family Rhodobacteraceae, were abundant both in cultures and in the wild, with their abundance positively correlated with that of picocyanobacteria.
ENVIRONMENTAL MICROBIOME
(2021)
Article
Microbiology
Anne E. Otwell, Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, Serdar Turkarslan, Sean M. Gibbons, Dwayne A. Elias, David A. Stahl, Gary Siuzdak, Nitin S. Baliga
Summary: Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is influenced by intermediates of nitrogen and sulfur cycling, such as hydrogen sulfide and nitrite. Mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of NRB have been uncovered through transcriptomic and metabolomic analyses, providing insights into the competitive interactions between NRB and SRB in diverse environments. The study highlights the importance of understanding how reduced sulfur compounds affect the growth and activity of NRB and SRB, impacting their stratification in different ecosystems.
Article
Biology
Christian Diener, Anna C. H. Hoge, Sean M. Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L. Moritz, Susan E. Erdman, Sean M. Gibbons
Summary: Broad spectrum antibiotics can cause both short-term and long-term damage to the ecology of the gut microbiome, leading to loss of bacterial diversity and increased susceptibility to infections. This study confirms the existence of whole-community tolerance phenotypes in murine gut influenced by antibiotic treatment duration or antimicrobial phytochemicals in diet. Future research should focus on identifying specific factors responsible for tipping communities between responder and non-responder phenotypes to protect microbiota from routine antibiotic treatment.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean M. Kearney, Katya Moniz, Mary Noel, Jeff Hooker, Sean M. Gibbons, Laure Segurel, Alain Froment, Rihlat Said Mohamed, Alain Fezeu, Vanessa A. Juimo, Sophie Lafosse, Francis E. Tabe, Catherine Girard, Deborah Iqaluk, Le Thanh Tu Nguyen, B. Jesse Shapiro, Jenni Lehtimaki, Lasse Ruokolainen, Pinja P. Kettunen, Tommi Vatanen, Shani Sigwazi, Audax Mabulla, Manuel Dominguez-Rodrigo, Yvonne A. Nartey, Adwoa Agyei-Nkansah, Amoako Duah, Yaw A. Awuku, Kenneth A. Valles, Shadrack O. Asibey, Mary Y. Afihene, Lewis R. Roberts, Amelie Plymoth, Charles A. Onyekwere, Roger E. Summons, Ramnik J. Xavier, Eric J. Alm
Summary: Industrialization has significant impacts on gene transfer in human gut bacteria, with higher rates of horizontal gene transfer (HGT) associated with industrialized lifestyles. This suggests that gut bacteria continuously acquire new functionality based on host lifestyle changes.
Article
Nutrition & Dietetics
Sean M. Gibbons, Thomas Gurry, Johanna W. Lampe, Anirikh Chakrabarti, Veerle Dam, Amandine Everard, Almudena Goas, Gross Gabriele, Michiel Kleerebez, Jonathan Lane, Johanna Maukonen, Ana Lucia Barretto Penna, Bruno Pot, Ana M. Valdes, Gemma Walton, Adrienne Weiss, Yoghatama Cindya Zanzer, Naomi V. Venlet, Michela Miani
Summary: This article provides an overview of computational and experimental tools used in microbiota-mediated personalized nutrition and health. It discusses the advances in in silico modeling, high-throughput in vitro techniques, and in vivo approaches for understanding personalized responses to diet and interventions. The article also highlights existing precision nutrition platforms and presents a vision of leveraging the gut microbiota for effective individual-specific interventions.
ADVANCES IN NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Kengo Watanabe, Tomasz Wilmanski, Christian Diener, John C. C. Earls, Anat Zimmer, Briana Lincoln, Jennifer J. J. Hadlock, Jennifer C. C. Lovejoy, Sean M. M. Gibbons, Andrew T. T. Magis, Leroy Hood, Nathan D. D. Price, Noa Rappaport
Summary: Multiomic profiling provides insights into the heterogeneity of metabolic states associated with obesity and changes in metabolic health. This study presents an atlas of blood analytes and their associations with body mass index (BMI), host polygenic risk scores, and gut microbiome composition. Machine learning models predict BMI more accurately using blood multiomics compared to BMI alone, and longitudinal analyses reveal variable BMI trajectories for different omics measures in response to a healthy lifestyle intervention. The findings highlight the importance of multiomics in quantifying metabolic health and predicting diseases.
Review
Microbiology
Christian Diener, Sean M. Gibbons
Summary: Microbial consortia play a crucial role in various essential processes, but it is challenging to understand their functional capacities based on their composition alone. Community-scale metabolic models have the potential to simulate complex microbial communities, but there is no consensus on the fitness function and community-wide growth. Transitioning from single-taxon models to multitaxon models poses challenges as well. Dynamic approaches are a solution but are computationally expensive, while two steady-state approaches provide ecologically relevant solutions with improved scalability.
Editorial Material
Microbiology
Christian Diener, Sean M. Gibbons
Summary: The composition of the human gut microbiome varies among individuals. However, by examining closely, common microbial genera can be identified that contribute significantly to this ecological variability. In this issue of Cell Host & Microbe, Frioux et al. present a method for identifying these bacterial guilds, also known as "enterosignatures."
CELL HOST & MICROBE
(2023)
Editorial Material
Biochemistry & Molecular Biology
Tomasz Wilmanski, Sean M. Gibbons
Summary: A recent study has shown that the ecological composition of the human gut virome changes with age, with a decline in core taxa and an enrichment of subdominant taxa, similar to what has been observed in the gut bacteriomes of centenarians.
TRENDS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Joe J. Lim, Christian Diener, James Wilson, Jacob J. Valenzuela, Nitin S. Baliga, Sean M. Gibbons
Summary: The authors present a novel approach for inferring in vivo growth phases of human gut bacteria from metagenomic time series data. These inferences can be used to better-constrain community scale metabolic modeling in the gut.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Tomasz Wilmanski, Sergey A. Kornilov, Christian Diener, Matthew P. Conomos, Jennifer C. Lovejoy, Paola Sebastiani, Eric S. Orwoll, Leroy Hood, Nathan D. Price, Noa Rappaport, Andrew T. Magis, Sean M. Gibbons
Summary: The composition of the gut microbiome is associated with patient responses to statin therapy. Specific microbiome compositions are related to the therapeutic effects and adverse reactions of statins. Further research may help utilize gut microbiome monitoring for precision statin treatment.
Article
Endocrinology & Metabolism
Christian Diener, Chengzhen L. Dai, Tomasz Wilmanski, Priyanka Baloni, Brett Smith, Noa Rappaport, Leroy Hood, Andrew T. Magis, Sean M. Gibbons
Summary: The study finds that a significant number of blood metabolites are associated with either host genetics or the gut microbiome, with a majority being driven by the microbiome. Furthermore, interaction effects between metabolite-microbe associations and specific genetic backgrounds are quite common.
Article
Endocrinology & Metabolism
Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C. Earls, Anat Zimmer, Gustavo Glusman, Max Robinson, James T. Yurkovich, Deborah M. Kado, Jane A. Cauley, Joseph Zmuda, Nancy E. Lane, Andrew T. Magis, Jennifer C. Lovejoy, Leroy Hood, Sean M. Gibbons, Eric S. Orwoll, Nathan D. Price
Summary: The study finds that as individuals age, the gut microbiome becomes increasingly unique, with this uniqueness strongly associated with microbially produced amino acid derivatives in the bloodstream. Healthy older individuals continue to show microbial drift towards a unique compositional state, while less healthy individuals do not. Retaining high levels of Bacteroides dominance or having a low gut microbiome uniqueness measure predicts decreased survival in a 4-year follow-up.
Review
Gastroenterology & Hepatology
Tomasz Wilmanski, Noa Rappaport, Christian Diener, Sean M. Gibbons, Nathan D. Price
Summary: This review discusses current approaches for defining and monitoring gut microbiome health, emphasizes the importance of identifying gut microbial ecological features resonant with host molecular phenotypes, and highlights certain gut microbial metabolites as potential biomarkers of gut microbiome health. It further explores how omics measurements and gut microbiome profiles can be integrated into sophisticated host-microbiome mechanistic models for personalized interventions.