Article
Agriculture, Dairy & Animal Science
Changgeng Yang, Ming Jiang, Xin Lu, Hua Wen
Summary: Dietary protein plays a crucial role in aquaculture, influencing the gut microbiota composition and metabolic profile in tilapia. Different protein levels in diets can impact the diversity and microbial composition of gut microbiota, as well as glycolysis and amino acid metabolism. The study highlights the importance of understanding the effects of dietary protein on fish health and cultivation practices.
Article
Biochemical Research Methods
Jorge Luis Galeano Nino, Hanrui Wu, Kaitlyn D. Lacourse, Harini Srinivasan, Matthew Fitzgibbon, Samuel S. Minot, Cassie Sather, Christopher D. Johnston, Susan Bullman
Summary: Single-cell RNA sequencing technologies have been beneficial in revealing cellular heterogeneity within mammalian tissues, including solid tumors. However, standard techniques have limited ability to capture microbial components of the tumor microenvironment. INVADEseq is a modified sequencing method that allows analysis of host-bacterial interactions at the single-cell level, making it a reliable tool for studying the tumor microenvironment.
Article
Biotechnology & Applied Microbiology
Andrea C. C. Timm, Bryan Brensinger, Meaghan Hart, Collin Timm, David Karig
Summary: The assembly and function of microbial communities are influenced by various factors, including the local environment and the metabolic properties of the colonizing organisms. Chemical communication and secreted factors also play a role in the cooperative and competitive interactions between different microbial strains. The secretions of microbes can have both positive and negative effects on their respective hosts, and understanding these effects can provide insights into microbiome function and lead to new intervention strategies. A microfluidic device is developed to enable high-content screening of microbial secretion effects on adherent cell types, allowing for scalable analysis of complex microbial communities and diverse host tissues.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Engineering, Environmental
Young Hwan Lee, Min-Sub Kim, Yoseop Lee, Chuxin Wang, Seong Chan Yun, Jae-Seong Lee
Summary: This study investigated the effects of interactions between microfibers and freshwater acidification (MFA) on individual Daphnia magna-microbiota interactions. The results showed that MFA interactions can have negative consequences on reproduction, growth, and sex ratio of D. magna, and can induce changes in immunity-and reproduction-related biological processes. The study also revealed that these adverse effects are closely related to changes in microbial communities, suggesting a causal link between D. magna fitness and the microbial community.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Review
Gastroenterology & Hepatology
Laura Grieneisen, Ran Blekhman, Elizabeth Archie
Summary: A crucial aspect of microbiome research is understanding how host genetics influence the composition of gut microbiota. However, it is challenging to establish a direct link between host genetics and gut microbiota composition due to the correlation between host genetic similarity and environmental similarity. Longitudinal microbiome data can offer valuable insights into the relative impact of genetic processes on the microbiome by revealing environmentally contingent host genetic effects and comparing genetic effects in different environments. This article explores four areas in which longitudinal data can provide new knowledge on host genetic effects on the microbiome: microbial heritability, microbial plasticity, microbial stability, and host and microbiome population genetics. Methodological considerations for future studies are also discussed.
Review
Oncology
Ramsha Mahmood, Athalia Voisin, Hana Olof, Reihane Khorasaniha, Samuel A. Lawal, Heather K. Armstrong
Summary: This review discusses the role of microbiomes in mediating interactions between dietary factors, inflammation, and different cancers. Dysbiosis, or disruptions in the microbiome, have been associated with various diseases including cancer. Understanding how different microbiomes interact with dietary factors can help improve interventions for cancer patients in the future.
Review
Immunology
Pilar Cornejo Ulloa, Bastiaan P. Krom, Monique H. van der Veen
Summary: Sex steroid hormones can affect both oral microbiota and host cells, potentially leading to oral health problems. Current research mainly focuses on the impact of hormonal changes on oral microorganisms, while broader studies have suggested new hypotheses about the effects of SSH.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Cell Biology
Justin A. Hayes, Anna W. Lunger, Aayushi S. Sharma, Matthew T. Fernez, Rebecca L. Carrier, Abigail N. Koppes, Ryan Koppes, Benjamin M. Woolston
Summary: This study successfully engineered a gut microphysiological model to titrate H2S gas and study the interactions between microbes and host cells. By visualizing in real time and analyzing gene expression, it was found that changes in H2S concentration led to alterations in host gene expression and metabolism.
Article
Biochemistry & Molecular Biology
Xi Zhang, Die Wang, Yafei Zheng, Yingxin Tu, Qingqing Xu, Haowei Jiang, Chen Li, Liangcai Zhao, Yuping Li, Hong Zheng, Hongchang Gao
Summary: The study reveals sexual dimorphism in T1D mice, with female mice showing greater changes in gut microbiota and male mice being more susceptible to T1D in terms of host metabolome. The correlation network analysis suggests that T1D-induced host metabolic changes may be regulated by the gut microbiota in a sex-specific manner, involving SCFAs metabolism, energy metabolism, amino acid metabolism, and choline metabolism.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2021)
Review
Microbiology
Mackenzie W. Gutierrez, Marie-Claire Arrieta
Summary: Recent studies have shown that the gut mycobiome also plays an important role in host health, with certain fungi potentially becoming stable colonizers in the gut and participating in host immunity and energy metabolism. Persistent fungal species like Candida, as well as less stable colonizers, have been shown to play an important role in host-mycobiome immune cross talk, but much of the mechanisms by which fungi interact with immune development remain elusive.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Review
Biochemical Research Methods
Andrea Galimberti, Antonia Bruno, Giulia Agostinetto, Maurizio Casiraghi, Lorenzo Guzzetti, Massimo Labra
Summary: Omics tools can characterize and trace fermented foods, while bioinformatics and biotechnological advances can enhance the nutritional value and sensory characteristics of these foods by assembling microbial artificial consortia, preserving traditional methods and local biodiversity.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Allergy
Haritz Irizar, Yoojin Chun, Zoe Arditi, Anh Do, Galina Grishina, Alexander Grishin, Alfin Vicencio, Supinda Bunyavanich
Summary: This study examined the associations between host genetics and nasal microbiome composition. The results showed that host genetics has little influence on nasal microbiome composition.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Microbiology
Dylan Baker, James Lauer, Anna Ortega, Sara L. Jackrel, Vincent J. Denef
Summary: Phytoplankton is crucial for life on Earth and its productivity is influenced by microbial communities in the phycosphere. Studying algal-bacterial interactions can help us understand the principles of algal-host interactions.
Article
Biochemical Research Methods
Vivek Ramanan, Shanti Mechery, Indra Neil Sarkar
Summary: This study developed a computational pipeline to analyze GenBank metadata and leveraged the collected dataset to shed light on compositional data practices and host-microbiome relationships. The dataset contains multiple kingdoms of microorganisms and hosts of multiple taxonomical classes, providing insights into host taxonomy and evolution.
Article
Biotechnology & Applied Microbiology
Hao Zhou, Juan Felipe Beltran, Ilana Lauren Brito
Summary: This study explores the potential mechanisms through which human-associated bacteria affect host health, with a focus on diseases such as IBD, CRC, obesity, and T2D. By leveraging publicly available data and analyzing metagenomic studies, the researchers identify differential targeting of bacterial genes that interact with human proteins involved in immune, oncogenic, apoptotic, and endocrine signaling pathways. This host-centric analysis provides valuable insights into the role of the microbiome in disease development.
Article
Biochemistry & Molecular Biology
Melissa Y. Chen, Jordan G. Kueneman, Antonio Gonzalez, Greg Humphrey, Rob Knight, Valerie J. McKenzie
Summary: Ecological community traits of host-associated microbiota can predict infection risk and intensity of pathogenic microbes, with richness and proportion being important predictors.
Article
Multidisciplinary Sciences
Brittany D. Needham, Masanori Funabashi, Mark D. Adame, Zhuo Wang, Joseph C. Boktor, Jillian Haney, Wei-Li Wu, Claire Rabut, Mark S. Ladinsky, Son-Jong Hwang, Yumei Guo, Qiyun Zhu, Jessica A. Griffiths, Rob Knight, Pamela J. Bjorkman, Mikhail G. Shapiro, Daniel H. Geschwind, Daniel P. Holschneider, Michael A. Fischbach, Sarkis K. Mazmanian
Summary: The integration of sensory and molecular inputs from the environment has a strong impact on animal behavior. This study focuses on the role of the gastrointestinal tract as a major site of exposure to environmental molecules. The gut microbiota plays a crucial role in behavior, neurotransmitter production, brain development, and myelination patterns in mice. The researchers identified specific genes in the gut microbiome that are responsible for the conversion of dietary tyrosine to a microbial metabolite called 4-ethylphenyl sulfate (4EPS). By engineering gut bacteria, they were able to selectively produce 4EPS in mice. The presence of 4EPS in the brain was associated with changes in activity and functional connectivity in specific brain regions. Furthermore, 4EPS impaired oligodendrocyte maturation in mice, leading to decreased myelination of neuronal axons and anxiety-like behaviors. The behavioral effects of 4EPS were prevented by promoting oligodendrocyte differentiation with pharmacological treatments. This study highlights the influence of a gut-derived molecule on complex behaviors through its effects on oligodendrocyte function and myelin patterning in the brain.
Article
Genetics & Heredity
Youwen Qin, Aki S. Havulinna, Yang Liu, Pekka Jousilahti, Scott C. Ritchie, Alex Tokolyi, Jon G. Sanders, Liisa Valsta, Marta Brozynska, Qiyun Zhu, Anupriya Tripathi, Yoshiki Vazquez-Baeza, Rohit Loomba, Susan Cheng, Mohit Jain, Teemu Niiranen, Leo Lahti, Rob Knight, Veikko Salomaa, Michael Inouye, Guillaume Meric
Summary: A study conducted on a large population-based cohort of 5,959 Finnish individuals identified genetic variations associated with gut microbial abundances. The study found 567 independent SNP-taxon associations, including associations with LCT, ABO, and MED13L genes. The findings shed light on the complex interactions between host genetics and gut microbiota, and their potential role in disease development.
Article
Nutrition & Dietetics
Julia Beauchamp-Walters, Gajender Aleti, Lourdes Herrera, Justine Debelius, Natalie Lima, Pritha Dalal, Suzi Hong, Rob Knight, Kyung E. Rhee
Summary: This study aimed to examine the relationship between diet and the gut microbiome in children with medical complexity (CMC) who receive enteral tube feedings, and to determine the impact of different formulas on the CMC microbiome. The results showed that CMC receiving exclusive enteral nutrition had decreased alpha diversity and differences in beta diversity compared with healthy controls, highlighting the importance of diet over medications.
JOURNAL OF PARENTERAL AND ENTERAL NUTRITION
(2023)
Article
Microbiology
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vazquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Meric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight
Summary: The operational genomic unit (OGU) method directly exploits sequence alignment hits to individual reference genomes for assessing microbial community diversity and relevance to environmental factors, offering maximal resolution of community composition and supporting phylogenetic methods. The method outperforms taxonomic unit-based analyses in informing biologically relevant insights, as demonstrated in real-world case studies.
Article
Microbiology
George Armstrong, Cameron Martino, Justin Morris, Behnam Khaleghi, Jaeyoung Kang, Jeff DeReus, Qiyun Zhu, Daniel Roush, Daniel McDonald, Antonio Gonazlez, Justin P. Shaffer, Carolina Carpenter, Mehrbod Estaki, Stephen Wandro, Sean Eilert, Ameen Akel, Justin Eno, Ken Curewitz, Austin D. Swafford, Niema Moshiri, Tajana Rosing, Rob Knight
Summary: This study tested the performance of recently developed computational tools Fastp and Minimap2 in metagenomics data preprocessing tasks and compared them with widely used choices Atropos and Bowtie2. The results showed that the new tools achieved faster processing, higher sensitivity, and minimal loss of specificity. Additionally, the taxonomic tables generated from downstream processing provided biologically comparable results. However, the study highlighted that Bowtie2's specificity is still necessary for taxonomic assignment. The authors suggest that regular reevaluation of pipeline components and improvements to standardized APIs can greatly enhance the efficiency of common bioinformatics tasks.
Article
Microbiology
Brandilyn A. Peters, Juan Lin, Qibin Qi, Mykhaylo Usyk, Carmen R. Isasi, Yasmin Mossavar-Rahmani, Carol A. Derby, Nanette Santoro, Krista M. Perreira, Martha L. Daviglus, Michelle A. Kominiarek, Jianwen Cai, Rob Knight, Robert D. Burk, Robert C. Kaplan
Summary: This study explores the relationship between menopause and the gut microbiome in a large Hispanic/Latino population. The findings suggest that postmenopausal women's gut microbiome becomes more similar to that of men, potentially due to the common condition of low estrogen/progesterone levels. Menopause also leads to specific changes in the gut microbiome, including a decrease in certain gut pathogens and a decrease in hormone-related metabolic potential. These changes in the gut microbiome are associated with adverse cardiometabolic risk in postmenopausal women.
Article
Gastroenterology & Hepatology
Geoffroy Mallaret, Amandine Lashermes, Mathieu Meleine, Ludivine Boudieu, Julie Barbier, Youssef Aissouni, Agathe Gelot, Benoit Chassaing, Andrew T. Gewirtz, Denis Ardid, Frederic Antonio Carvalho
Summary: This study aimed to investigate the mechanisms between early life events and the development of colonic hypersensitivity (CHS). Maternal separation model (NMS) was used to mimic deleterious events in childhood. Results showed that around 50% of NMS mice exhibited increased intestinal permeability and CHS associated with intestinal dysbiosis. Furthermore, only TLR5 mRNA expression was increased in colonocytes of NMS mice with CHS. Acute intrarectal instillation of TLR5 agonist also induced transient CHS appearance.
WORLD JOURNAL OF GASTROENTEROLOGY
(2022)
Review
Gastroenterology & Hepatology
Bernard Srour, Melissa C. Kordahi, Erica Bonazzi, Melanie Deschasaux-Tanguy, Mathilde Touvier, Benoit Chassaing
Summary: This review provides an overview of the current data that highlight the association between ultra-processed food consumption and various chronic diseases, with a focus on epidemiological evidence and mechanistic insights involving the intestinal microbiota.
LANCET GASTROENTEROLOGY & HEPATOLOGY
(2022)
Editorial Material
Microbiology
Benoit Chassaing
Summary: Loss-of-function mutations in NOD2, a receptor-sensing microbiota-derived muropeptides, predispose individuals to Crohn's disease (CD). In this study, Gao et al. (2022) identify a microbiota-derived peptidoglycan remodeling enzyme that suppresses chronic intestinal inflammation via NOD2, potentially providing a pathway for alleviating CD.
CELL HOST & MICROBE
(2022)
Article
Gastroenterology & Hepatology
Noemie Daniel, Andrew T. Gewirtz, Benoit Chassaing
Summary: The study shows that the food additives carboxymethylcellulose (CMC) and polysorbate 80 (P80) can negatively impact intestinal microbiota, leading to chronic low-grade inflammation and metabolic dysregulations. However, daily administration of the probiotic Akkermansia muciniphila (A.muciniphila) can protect against the detrimental effects of these additives on both the microbiota and host. This study highlights the potential of using A.muciniphila as a probiotic to maintain intestinal and metabolic health.
Editorial Material
Gastroenterology & Hepatology
Jeremy Denizot, Benoit Chassaing
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Cell Biology
Noemie Daniel, Melanie Le Barz, Patricia L. Mitchell, Thibault V. Varin, Isabelle Bourdeau Julien, Dominique Farabos, Genevieve Pilon, Josee Gauthier, Carole Garofalo, Jing X. Kang, Jocelyn Trottier, Olivier Barbier, Denis Roy, Benoit Chassaing, Emile Levy, Frederic Raymond, Antonin Lamaziere, Nicolas Flamand, Cristoforo Silvestri, Christian Jobin, Vincenzo Di Marzo, Andre Marette
Summary: We compared endogenous omega-3 PUFA production to supplementation and found that endogenous production improved glucose intolerance and insulin resistance, while supplementation prevented hepatic steatosis but failed to improve insulin resistance.
Article
Nutrition & Dietetics
Jean-Baptiste Bizeau, Mayssa Albouery, Stephane Gregoire, Benedicte Buteau, Lucy Martine, Marine Crepin, Alain M. Bron, Olivier Berdeaux, Niyazi Acar, Benoit Chassaing, Marie-Agnes Bringer
Summary: This study investigated the impact of dietary intake of inulin on the levels of plasmalogens in the mouse cortex. The results showed that inulin supplementation reduced the abundance of ethanolamine plasmalogens in the cortex, but had no effect on enzyme gene expression or fatty acid profile.
Meeting Abstract
Gastroenterology & Hepatology
Alexis Bretin, Jun Zou, Michael Pellizzon, Benoit Chassaing, Andrew T. Gewirtz