Article
Biotechnology & Applied Microbiology
Giulia Alessandri, Federico Fontana, Leonardo Mancabelli, Gabriele Andrea Lugli, Chiara Tarracchini, Chiara Argentini, Giulia Longhi, Alice Viappiani, Christian Milani, Francesca Turroni, Douwe van Sinderen, Marco Ventura
Summary: In vitro gut cultivation models were used to study the effects of intrinsic and extrinsic factors on the infant gut microbiota, resulting in the optimization of a medium (IGSM) that maintains its biodiversity. The study also evaluated the impact of two pediatric drugs on the taxonomic composition of the infant gut microbiota.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Nutrition & Dietetics
Mary E. Kable, Elizabeth L. Chin, Liping Huang, Charles B. Stephensen, Danielle G. Lemay
Summary: The study aimed to estimate lactose consumption and explore the interaction between lactose consumption, LP genotype, and gut microbiome in healthy adults in the US. The results showed that individuals with the LNP genotype consumed more lactose and had increased abundance of Lactobacillaceae and Lachnospiraceae taxa.
JOURNAL OF NUTRITION
(2023)
Article
Microbiology
Falk Hildebrand, Toni Gossmann, Clemence Frioux, Ezgi Ozkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjorn Nielsen, Peer Bork
Summary: Human gut bacterial strains can persist for decades in individuals, families, and geographic regions, with locally successful strains of Bacteroidota showing high levels of genetic adaptation. By contrast, Firmicutes rely on weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses provide insights into long-term persistence of gut microbes and the implications for gut flora modulations.
CELL HOST & MICROBE
(2021)
Article
Gastroenterology & Hepatology
M. A. Azcarate-Peril, J. Roach, A. Marsh, William D. Chey, William J. Sandborn, Andrew J. Ritter, Dennis A. Savaiano, T. R. Klaenhammer
Summary: The study confirmed the significant symptom reduction and alteration of fecal microbiome in lactose intolerant patients with the administration of pure galacto-oligosaccharides. The analysis further suggested long-term benefits when individuals continued consumption of dairy products after the treatment.
Article
Nutrition & Dietetics
Junying Zhao, Wei Yi, Bin Liu, Yaohua Dai, Tiemin Jiang, Shuxing Chen, Jianwu Wang, Baowen Feng, Weicang Qiao, Yanpin Liu, Huihuang Zhou, Jianying He, Juncai Hou, Lijun Chen
Summary: This study shows that breastfed infants have a higher abundance of Bifidobacterium in their gut microbiota compared to formula-fed infants. The microbiome shifts in stool were associated with changes in urine metabolites. Key components of MFGM were significantly positively correlated with Bifidobacterium in stool samples, and stimulated its growth rate in vitro.
EUROPEAN JOURNAL OF NUTRITION
(2022)
Article
Ecology
Weizhong Li, Karen E. Nelson
Summary: Recent studies suggest that many species of human gut microbiota acquired in early childhood can persist into senior adulthood, with some species showing a higher likelihood of being shared between twins, indicating a potential genetic component in microbiota transmission.
Article
Biochemistry & Molecular Biology
Mingzhu Du, Xinqiang Xie, Shuanghong Yang, Ying Li, Tong Jiang, Juan Yang, Longyan Li, Yunxiao Huang, Qingping Wu, Wei Chen, Jumei Zhang
Summary: This study identified a lysozyme-like protein from Bifidobacterium longum and confirmed its bioactivity in delaying the growth of certain bacteria. The protein significantly affected the composition of the human gut microbiota, indicating its potential role as a regulatory factor in communicating with intestinal microbes.
Article
Biochemistry & Molecular Biology
Tommi Vatanen, Qi Yan Ang, Lea Siegwald, Shafiqul Alam Sarker, Caroline Le Roy, Stephane Duboux, Omar Delannoy-Bruno, Catherine Ngom-Bru, Claire L. Boulange, Martin Strazar, Julian Avila-Pacheco, Amy Deik, Kerry Pierce, Kevin Bullock, Courtney Dennis, Shamima Sultana, Sharika Sayed, Mahbubar Rahman, Tahmeed Ahmed, Monica Modesto, Paola Mattarelli, Clary B. Clish, Hera Vlamakis, Damian R. Plichta, Olga Sakwinska, Ramnik J. Xavier
Summary: This study investigated the gut microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. It found that a specific Bifidobacterium longum clade expanded after the introduction of solid foods and had enzymes for utilizing both breast milk and solid food substrates. The clade was prevalent in Bangladesh, present globally (at lower prevalence), and correlated with other gut taxa and metabolites, indicating its important role in gut ecology.
Article
Clinical Neurology
Shourong Lu, Ying Yang, Qiao Xu, Shuqiang Wang, Jie Yu, Bingshan Zhang, Zhuo Wang, Yunyun Zhang, Wenwei Lu, Kan Hong
Summary: This study identified gut microbial markers associated with cognitive impairment (CI) and developed a machine learning model for predicting CI. The results showed significant differences in gut microbial composition and functions between the control and CI groups. Several genera were identified as potential markers for CI. These findings provide potential diagnostic tools for preventing the development of CI in the elderly.
FRONTIERS IN NEUROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anastasia Revel-Muroz, Mikhail Akulinin, Polina Shilova, Alexander Tyakht, Natalia Klimenko
Summary: The stability of the gut microbiome is crucial for maintaining its functional richness. This study compares the outcomes of mathematical modelling and statistical analysis in investigating the stability of the microbiome. The results show a significant correlation between the two approaches and confirm the inverse relationship between robustness and local stability.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Microbiology
Florencia Velez-Cortes, Harris Wang
Summary: Bacterially secreted proteins are crucial for the functioning of bacterial cells and communities. In this study, a computational pipeline was used to predict and analyze the bacterial metasecretome of the human gut, revealing the presence of diverse families of secreted carbohydrate-active enzymes and their distribution across taxonomic groups. By mapping secreted proteins to metagenomic data from endoscopic sampling of the human gastrointestinal tract, specific regions were identified where resident microbes secrete glycosidases. The comprehensive analysis of the metasecretome provides valuable insights for microbiome research and understanding the impact of gut bacteria on human health.
Article
Food Science & Technology
Liv R. Dedon, Margaret A. Hilliard, Asha Rani, Zunny Tatiana Daza-Merchan, Galaxie Story, Carrie-Ellen Briere, David A. Sela
Summary: This study investigates the effect of fucosylated human milk oligosaccharides (fHMOs) on the gut microbiota of infants. The results show that the structure of fHMOs influences the composition of the gut microbiome, but has minimal impact on the production of short chain fatty acids.
MOLECULAR NUTRITION & FOOD RESEARCH
(2023)
Article
Nutrition & Dietetics
Jong-Wook Yoo, Yoon-Jung Shin, Xiaoyang Ma, Young-Hoo Son, Hyo-Min Jang, Chang Kyun Lee, Dong-Hyun Kim
Summary: Gut microbiota dysbiosis is closely related to psychiatric disorders and inflammatory bowel disease. The transplantation of Enterobacteriaceae-rich gut microbiota can cause depression and colitis in mice. However, treatment with anti-inflammatory probiotics can alleviate these symptoms.
Article
Allergy
Antti E. Seppo, Kevin Bu, Madina Jumabaeva, Juilee Thakar, Rakin A. Choudhury, Chloe Yonemitsu, Lars Bode, Camille A. Martina, Maria Allen, Sabrina Tamburini, Enrica Piras, David S. Wallach, R. John Looney, Jose C. Clemente, Kirsi M. Jarvinen
Summary: The study found a higher colonization rate of B. infantis in rural OOM infants at low risk for atopic diseases, similar to rates seen in developing countries. These infants' stool samples had higher levels of lactate and medium- to long/odd-chain fatty acids.
Article
Gastroenterology & Hepatology
Jingjing Wang, Jinlong Qie, Danrong Zhu, Xuemei Zhang, Qingqing Zhang, Yuyu Xu, Yipeng Wang, Kai Mi, Yang Pei, Yang Liu, Guozhong Ji, Xingyin Liu
Summary: This study investigated the dynamic characteristics of gut microbiome associated with longevity, neural, and immune function decline. The results showed that centenarians had increased diversity of gut microbiota, damaged connection among bacteria, and an enrichment of potential probiotic species, such as Bifidobacterium pseudocatenulatum. Changes in neural function markers (A beta and BDNF) and increased inflammatory factors were also observed. Therefore, this study provides a theoretical basis for targeting the gut microbiome in future treatments of aging-related diseases and extending lifespan.
Article
Microbiology
Jacobo de la Cuesta-Zuluaga, Tim D. Spector, Nicholas D. Youngblut, Ruth E. Ley
Summary: Archaea of the order Methanomassiliicoccales use methylated amines such as trimethylamine as substrates for methanogenesis. Genomic adaptations differ by clade, not habitat preference, indicating convergent evolution between the clades. In the human gut, Methanomassiliicoccales are correlated with trimethylamine-producing bacteria but were not detected in all human populations.
Article
Microbiology
Xiaoying Liu, Jessica L. Sutter, Jacobo de la Cuesta-Zuluaga, Jillian L. Waters, Nicholas D. Youngblut, Ruth E. Ley
Summary: The genera Catabacter and Christensenella, both strict anaerobes within the Firmicutes phylum, are closely related. Phylogenetic analysis shows that Catabacter splits Christensenella into a polyphyletic clade. Based on evolutionary relationship, Catabacter hongkongensis should be transferred to the genus Christensenella as Christensenella hongkongensis comb. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Daphne K. Welter, Albane Ruaud, Zachariah M. Henseler, Hannah N. De Jong, Peter Van Coeverden de Groot, Johan Michaux, Linda Gormezano, Jillian L. Waters, Nicholas D. Youngblut, Ruth E. Ley
Summary: Psychrobacter genus strains exhibit different growth patterns and characteristics, and were detected in polar bear fecal samples, but only one group of strains persisted in the gut of gnotobiotic mice in experiments.
Article
Multidisciplinary Sciences
Nicholas D. Youngblut, Ruth E. Ley
Summary: Mapping metagenome reads to reference databases is a standard approach for assessing microbial taxonomic and functional diversity. However, public reference databases often lack recently generated genomic data, limiting the sensitivity of readmapping. In order to address this issue and improve database comprehensiveness, the authors developed a faster database generation method, Struo2, along with custom databases that can be easily updated with new genomic content.
Editorial Material
Biochemistry & Molecular Biology
James W. Marsh, Ruth E. Ley
Article
Microbiology
Nicholas D. Youngblut, Jacobo De La Cuesta-Zuluaga, Ruth E. Ley
Summary: Tree-based diversity measures improve the identification of explanatory factors in microbial communities and provide unique insight into microbiome diversity partitioned by phenotype. They greatly improve machine learning model performance in predicting phenotype.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Editorial Material
Multidisciplinary Sciences
Taichi A. Suzuki, Ruth E. Ley
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Hagay Enav, Fredrik Baeckhed, Ruth E. Ley
Summary: The colonization of the infant microbiome is a complex process influenced by ecological forces and environmental conditions. Recent advancements in strain-level analysis have revealed the immense complexity of the system, providing a better understanding of how strains of the same species spread, colonize, evolve, and impact the host.
CELL HOST & MICROBE
(2022)
Article
Gastroenterology & Hepatology
Benoit Chassaing, Charlene Compher, Brittaney Bonhomme, Qing Liu, Yuan Tian, William Walters, Lisa Nessel, Clara Delaroque, Fuhua Hao, Victoria Gershuni, Lillian Chau, Josephine Ni, Meenakshi Bewtra, Lindsey Albenberg, Alexis Bretin, Liam McKeever, Ruth E. Ley, Andrew D. Patterson, Gary D. Wu, Andrew T. Gewirtz, James D. Lewis
Summary: In healthy adults, consumption of the synthetic emulsifier CMC was found to exacerbate postprandial abdominal discomfort, disrupt gut microbiota and metabolome composition, leading to reduced diversity, and possibly contributing to the development of chronic inflammatory diseases.
Article
Microbiology
Stacey L. Heaver, Henry H. Le, Peijun Tang, Arnaud Basle, Claudia Mirretta Barone, Dai Long Vu, Jillian L. Waters, Jon Marles-Wright, Elizabeth L. Johnson, Dominic J. Campopiano, Ruth E. Ley
Summary: This study characterizes the pathways responsible for inositol lipid production in human gut Bacteroides and explores the importance of these lipids for capsule expression, antimicrobial peptide resistance, and colonization. The authors identify the biosynthetic pathway and enzymes involved in inositol lipid synthesis, and show that loss of inositol lipid production affects bacterial fitness and symbiosis in a mouse model. They also discover a previously undescribed pathway for bacterial PI-DAG synthesis. Overall, the findings suggest that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiotic relationships.
NATURE MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Taichi A. Suzuki, J. Liam Fitzstevens, Victor T. Schmidt, Hagay Enav, Kelsey E. Huus, Mirabeau Mbong Ngwese, Anne Griesshammer, Anne Pfleiderer, Bayode R. Adegbite, Jeannot F. Zinsou, Meral Esen, Thirumalaisamy P. Velavan, Ayola A. Adegnika, Le Huu Song, Timothy D. Spector, Amanda L. Muehlbauer, Nina Marchi, Hyena Kang, Lisa Maier, Ran Blekhman, Laure Segurel, GwangPyo Ko, Nicholas D. Youngblut, Peter Kremsner, Ruth E. Ley
Summary: The gut microbiomes of human populations worldwide have common core microbial species. However, within a species, certain strains show population specificity. This study suggests that humans and their gut microbes have experienced parallel evolutionary history, and specific microbial strains may play a crucial role in microbiome-mediated disease phenotypes.
Article
Gastroenterology & Hepatology
Yishay Pinto, Sigal Frishman, Sondra Turjeman, Adi Eshel, Meital Nuriel-Ohayon, Oshrit Shrossel, Oren Ziv, William Walters, Julie Parsonnet, Catherine Ley, Elizabeth L. Johnson, Krithika Kumar, Ron Schweitzer, Soliman Khatib, Faiga Magzal, Efrat Muller, Snait Tamir, Kinneret Tenenbaum-Gavish, Samuli Rautava, Seppo Salminen, Erika Isolauri, Or Yariv, Yoav Peled, Eran Poran, Joseph Pardo, Rony Chen, Moshe Hod, Elhanan Borenstein, Ruth E. Ley, Betty Schwartz, Yoram Louzoun, Eran Hadar, Omry Koren
Summary: This study comprehensively analyzed the gut microbiome, metabolome, inflammatory cytokines, nutrition, and clinical records of 394 women during the first trimester of pregnancy in order to predict the onset of gestational diabetes mellitus (GDM) earlier than currently accepted. The study also demonstrated the role of the gut microbiome in the development of GDM. These findings provide potential targets for early diagnostics and therapeutic intervention in the prevention of GDM.
Article
Biochemical Research Methods
Albane Ruaud, Niklas Pfister, Ruth E. Ley, Nicholas D. Youngblut
Summary: Tree ensemble machine learning models are increasingly used in microbiome science due to their compatibility with the structure of sequence-based microbiome data. The endoR method simplifies and interprets these models, providing insights into the importance of features and their interactions. Through validations, endoR has shown comparable accuracy to other approaches and has been successfully applied to study the gut microbiome and identify associations between microbial taxa.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
William A. Walters, Andrea C. Granados, Catherine Ley, Scot Federman, Doug Stryke, Yale Santos, Thomas Haggerty, Alicia Sotomayor-Gonzalez, Venice Servellita, Ruth E. Ley, Julie Parsonnet, Charles Y. Chiu
Summary: The human gut virome and its early life development are not well understood. This study used viral metagenomic sequencing to examine the virome composition of infants and their mothers longitudinally. It was found that the infant virome primarily consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, while the maternal virome had a larger presence of undetected vertebrate viruses. The development of the infant virome was mainly influenced by dietary, infectious, and environmental factors rather than direct maternal acquisition.
CELL HOST & MICROBE
(2023)
Article
Gastroenterology & Hepatology
Jacobo de la Cuesta-zuluaga, Kelsey E. Huus, Nicholas D. Youngblut, Juan S. Escobar, Ruth E. Ley
Summary: Obesity and cardiometabolic disease are associated with changes in the gut microbiome. Through studying a cohort of 408 adults from Colombia, researchers validated previously reported features of the gut microbiome function and diversity correlated with obesity or poor cardiometabolic health status. The results showed that obesity, rather than metabolic status, is the main driver of differences in gut microbiome functions and structure in individuals with or without poor cardiometabolic health.