Article
Endocrinology & Metabolism
Dong D. Wang, Qibin Qi, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Alvarez, Josiemer Mattei, Martha Tamez, Marc D. Gellman, Martha Daviglus, Frank B. Hu, Meir J. Stampfer, Curtis Huttenhower, Rob Knight, Robert D. Burk, Robert C. Kaplan
Summary: This study reveals that adherence to the Mediterranean diet can affect gut microbiome composition and functions. The association between the Mediterranean diet and diabetes prevalence varies depending on individual gut microbial composition.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Article
Evolutionary Biology
William R. Shoemaker, Daisy Chen, Nandita R. Garud
Summary: Genetic variation in the human gut microbiome plays a crucial role in various phenotypes. However, our understanding of its origins and maintenance is limited. By comparing evolutionary processes across different species, we can identify universal trends and deviations. The human gut microbiome offers unparalleled potential for comparative population genomics studies.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Isabelle Bourdeau-Julien, Sophie Castonguay-Paradis, Gabrielle Rochefort, Julie Perron, Benoit Lamarche, Nicolas Flamand, Vincenzo Di Marzo, Alain Veilleux, Frederic Raymond
Summary: This study aimed to investigate the effects of a lead-in diet on the response to a short-term dietary intervention. The results showed that dietary changes had an immediate and reversible modulation on gut microbiota composition, endocannabinoidome mediators, short-chain fatty acids, and branched-chain fatty acids. The response of gut microbiota composition was more influenced by the lead-in diet, while the endocannabinoidome response was not affected. Higher initial microbiome diversity favored the stability of gut microbiota in response to dietary changes.
Article
Multidisciplinary Sciences
R. Gacesa, A. Kurilshikov, A. Vich Vila, T. Sinha, M. A. Y. Klaassen, L. A. Bolte, S. Andreu-Sanchez, L. Chen, V. Collij, S. Hu, J. A. M. Dekens, V. C. Lenters, J. R. Bjork, J. C. Swarte, M. A. Swertz, B. H. Jansen, J. Gelderloos-Arends, S. Jankipersadsing, M. Hofker, R. C. H. Vermeulen, S. Sanna, H. J. M. Harmsen, C. Wijmenga, J. Fu, A. Zhernakova, R. K. Weersma
Summary: This study analyzed the gut microbiome of 8,208 individuals from the Netherlands and found that the microbiome is primarily shaped by the environment and cohabitation. Only about 6.6% of microbial taxa are heritable, while around 48.6% of taxa are significantly influenced by cohabitation. Additionally, the study identified numerous associations between the microbiome and health, diet, socioeconomic factors, and early-life and current exposome.
Article
Microbiology
Viviana J. Mancilla, Allison E. Mann, Yan Zhang, Michael S. Allen
Summary: This study revealed differences in gut bacterial communities between phenylketonuria (PKU) patients and non-PKU controls, with lower diversity and statistically differentially abundant genera in PKU individuals. Furthermore, metabolic pathways also differed between the two groups, highlighting the need for further research on the effects of dietary restrictions.
Article
Microbiology
Julien Tap, Stine Storsrud, Boris Le Neve, Aurelie Cotillard, Nicolas Pons, Joel Dore, Lena Ohman, Hans Tornblom, Muriel Derrien, Magnus Simren
Summary: Individuals with severe IBS were found to have a higher intake of poorer-quality food items, and the covariations between gut microbiota at subspecies level and diet were associated with factors such as symptom severity. The study provides insight into diet-microbiota-symptom interactions and may guide future interventional studies on gut microbiome-based nutritional recommendations for managing gastrointestinal symptoms.
Article
Gastroenterology & Hepatology
Barbara Olendzki, Vanni Bucci, Caitlin Cawley, Rene Maserati, Margaret McManus, Effie Olednzki, Camilla Madziar, David Chiang, Doyle Ward, Randall Pellish, Christine Foley, Shakti Bhattarai, Beth A. McCormick, Ana Maldonado-Contreras
Summary: This study aims to investigate the impact of specific foods on the intestinal microbiome in patients with IBD and explore the interactions between diet and immunity to provide personalized nutrition guidance for IBD patients with dysbiosis-related conditions.
Article
Multidisciplinary Sciences
Brian K. Trevelline, Kevin D. Kohl
Summary: This study demonstrates that the gut microbiome can influence host diet selection behavior by mediating the availability of essential amino acids, revealing a mechanism by which gut microbiota can regulate host foraging behavior.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Charli S. Davies, Sarah F. Worsley, Kathryn H. Maher, Jan Komdeur, Terry Burke, Hannah L. Dugdale, David S. Richardson
Summary: This study found that components of the host's immune system, specifically MHC-I and MHC-II variation, can influence the diversity and composition of the gut microbiome. This suggests that host-microbiome coevolution may play a role in maintaining immunogenetic variation within populations.
Article
Medicine, General & Internal
Claudia Cantoni, Qingqi Lin, Yair Dorsett, Laura Ghezzi, Zhongmao Liu, Yeming Pan, Kun Chen, Yanhui Han, Zhengze Li, Hang Xiao, Matthew Gormley, Yue Liu, Suresh Bokoliya, Hunter Panier, Cassandra Suther, Emily Evans, Li Deng, Alberto Locca, Robert Mikesell, Kathleen Obert, Pamela Newland, Yufeng Wu, Amber Salter, Anne H. Cross, Phillip Tarr, Amy Lovett-Racke, Laura Piccio, Yanjiao Zhou
Summary: This study conducted a six-month longitudinal multi-omics study on multiple sclerosis (MS) patients and healthy controls, revealing multi-system alterations in gut microbiota, immune system, and blood metabolome. The study demonstrated the interactions between gut microbiome and host immune system, metabolism, and diet, and identified microbiome and metabolome features related to the degree of disability in MS patients. Furthermore, a correlation network linking meat intake with gut microbiota and blood metabolites was discovered.
Review
Microbiology
JamesW. Marsh, Christian Kirk, Ruth E. Ley
Summary: Genetic manipulation is necessary to study microorganisms in their environments, but many species in the human gut microbiome are not genetically tractable. This review addresses the barriers to genetic techniques for gut microbes and discusses ongoing efforts to develop genetic systems. While there is promise in methods that aim to genetically transform multiple species simultaneously, they still face challenges. Increasing the genetic tractability of gut microbiome species is a top priority for microbiome research and will enable microbiome engineering.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Ecology
Siddiq Akbar, Xianxian Li, Zihao Ding, Qi Liu, Jing Huang, Qiming Zhou, Lei Gu, Zhou Yang
Summary: The study demonstrates that the microbiome of Daphnia is flexible and varies with genotype, diet, and medium-associated microbes. Not all bacteria are beneficial to Daphnia, and only symbionts can increase Daphnia performance.
Review
Gastroenterology & Hepatology
Gertrude Ecklu-Mensah, Jack Gilbert, Suzanne Devkota
Summary: Diet plays a crucial role in shaping the gut microbiota, with dietary selection pressures throughout life influencing the composition and diversity of microorganisms. Personalized dietary solutions should be tailored to an individual's personal history and nutritional needs.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Gastroenterology & Hepatology
Pajau Vangay, Tonya Ward, Sarah Lucas, Lalit K. Beura, Dominique Sabas, Max Abramson, Lisa Till, Susan L. Hoops, Purna Kashyap, Ryan C. Hunter, David Masopust, Dan Knights
Summary: In this study, the differential effects of human gut microbiota from the United States and rural Thailand on the murine gut mucosa and immune system were assessed. The results suggest that Western-associated human gut microbes contribute to a pro-inflammatory immune response.
Article
Nutrition & Dietetics
Kirra Borrello, Unhee Lim, Song-Yi Park, Kristine R. Monroe, Gertraud Maskarinec, Carol J. Boushey, Lynne R. Wilkens, Timothy W. Randolph, Loic Le Marchand, Meredith A. Hullar, Johanna W. Lampe
Summary: This study found that racial/ethnic differences in GM composition may be influenced by differences in diet. Overall diet quality and intake of certain foods were found to have significant effects on GM composition, which may contribute to racial/ethnic health disparities.
Article
Fisheries
Lucilla Giulietti, Egil Karlsbakk, Paolo Cipriani, Miguel Bao, Julia E. Storesund, Nachiket P. Marathe, Arne Levsen
Summary: This study examined the occurrence of 'soft flesh' in Northeast Atlantic autumn mackerel caught between 2007 and 2020, and investigated the prevalence and density of the myxosporean parasite Kudoa thyrsites and its relation to 'soft flesh'. The occurrence of 'soft flesh' remained stable for a decade but increased significantly in 2019 and 2020. The study also found that the prevalence of the parasite is higher than the occurrence of 'soft flesh' and only individuals with high parasite density showed the condition. qPCR analysis should be used to estimate the prevalence of K. thyrsites and assess the risk of 'soft flesh' in NEA mackerel.
FISHERIES RESEARCH
(2023)
Article
Public, Environmental & Occupational Health
Fredrik Hakonsholm, Marit A. K. Hetland, Cecilie S. Svanevik, Bjorn Tore Lunestad, Iren H. Lohr, Nachiket P. Marathe
Summary: This study investigates the genetic diversity, resistome, and pathogenic potential of Kp isolates from the Norwegian marine environment using whole-genome sequencing. The study provides the first comprehensive account of genetic diversity among Kp from the marine environment and reveals a high diversity of Kp in the Norwegian marine environment and seafood, including globally disseminated pathogenic sequence types carrying clinically relevant antibiotic resistance genes and virulence factors, as well as several heavy metal resistance genes.
INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH
(2022)
Article
Biotechnology & Applied Microbiology
Sudarshan A. Shetty, Ben Kuipers, Siavash Atashgahi, Steven Aalvink, Hauke Smidt, Willem M. de Vos
Summary: Knowledge of functional roles and interspecies interactions in the human intestinal microbiome is crucial. This study provides insights into the complex metabolic interactions between core intestinal bacterial species and the production of key short chain fatty acids.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Ecology
Sudarshan A. Shetty, Ioannis Kostopoulos, Sharon Y. Geerlings, Hauke Smidt, Willem M. de Vos, Clara Belzer
Summary: This study investigates the ecological and metabolic interactions of 16 key bacteria in the human gut using a synthetic minimal microbiome, revealing crucial insights into their co-existence, metabolic niches, and trophic roles in a highly dynamic and competitive in vitro ecosystem.
Article
Parasitology
Lucilla Giulietti, Heidi Johansen Nedberg, Egil Karlsbakk, Nachiket P. Marathe, Julia E. Storesund, Stig Maehle, Ingrid Uglenes Fiksdal, Dawit Berhe Ghebretnsae, Arne Levsen
Summary: This study examined the distribution of K. thyrsites in various organs of NEA mackerel and found that the parasite has the highest density in the musculature. The study also revealed a weak positive correlation between the parasite density in the muscle and the extent of myoliquefaction. Histological examinations showed an association between the dispersion of free myxospores and the level of muscle myoliquefaction.
PARASITOLOGY RESEARCH
(2022)
Article
Cell Biology
Alper Cevirgel, Sudarshan A. Shetty, Martijn Vos, Nening M. Nanlohy, Lisa Beckers, Elske Bijvank, Nynke Rots, Josine van Beek, Anne-Marie Buisman, Debbie van Baarle
Summary: Immunosenescence refers to immune dysfunction observed in older individuals. To better understand this phenomenon, we investigated immune cell subsets and variation in the aging population. We identified nine immunotypes that displayed different aging-related immune signatures, which explained inter-individual variation better than age. Additionally, we found that immune stability was lower in immunotypes containing aging-associated immune subsets and correlated with an increase in circulating CD38 + CD4+ T follicular helper cells after influenza vaccination.
Article
Infectious Diseases
Priyank S. Nimje, Nachiket P. Marathe
Summary: The aim of this study was to understand the genetic basis of resistance to fi-lactam antibiotics in Vibrio anguillarum isolates obtained from Atlantic mackerel, and to identify a novel fi-lactamase (VAN-1) from these isolates using whole genome sequencing. The results showed that a novel fi-lactamase gene blaVAN-1, which shares nucleotide identity with a known mobile fi-lactamase from Vibrio species, was detected in the isolates. The study highlights the importance of the marine environment as a reservoir of new antibiotic resistance genes and suggests the potential for long-distance transport of antibiotic resistance determinants by migratory fish.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2023)
Article
Microbiology
Daniel Jaen-Luchoro, Roger Karlsson, Antonio Busquets, Beatriz Pineiro-Iglesias, Nahid Karami, Nachiket P. Marathe, Edward R. B. Moore
Summary: Resistance to beta-lactams is a complex and multifactorial process in bacteria. This study aimed to develop a system to assess the phenotypic and proteomic responses of bacteria to antibiotic stress caused by the loss of specific antimicrobial resistance genes. Through knocking out plasmid-borne beta-lactamase genes in Escherichia coli, the knockout variants lacking the targeted beta-lactamases were generated. Proteomic analyses showed that the loss of bla(CTX-M-15) gene had the greatest impact on protein expression dynamics, while the losses of bla(OXA-1) and bla(TEM-1) had a lesser effect. The study provides insights into the genomic, proteomic, and phenotypic impacts of resistance gene loss.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Nachiket P. Marathe, Francisco Salva-Serra, Priyank S. Nimje, Edward R. B. Moore
Summary: In this study, Shewanella baltica strains isolated from the gut contents of wild Atlantic mackerel were analyzed using whole-genome sequencing. The study identified new variants of antibiotic resistance genes and found the presence of the mobile colistin resistance gene mcr-4.3 in a significant proportion of the strains. The analysis of the complete genome sequence of one strain further revealed the presence of multiple plasmids carrying different resistance genes. This study provides insights into the genetic diversity and mobility of antibiotic resistance genes in Shewanella spp., highlighting the importance of the marine environment in the emergence and dissemination of clinically important resistance genes.
MICROBIOLOGY SPECTRUM
(2022)
Article
Public, Environmental & Occupational Health
Nachiket P. Marathe, Didrik H. Grevskott, Francisco Salva-Serra, Priyank S. Nimje, Cecilie S. Svanevik, Bjorn Tore Lunestad, Edward R. B. Moore
Summary: This study found clinically-important multidrug-resistant conjugative plasmids in seawater samples from Bergen harbor. These plasmids carry various resistance genes and virulence factors, posing a potential risk of transmission to human microbiota. The results highlight the need for surveillance of antibiotic resistance, as suggested by the World Health Organization, even in low prevalence settings like Norway.
INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH
(2023)
Article
Public, Environmental & Occupational Health
Vera Radisic, Didrik H. Grevskott, Bjorn Tore Lunestad, Lise Ovreas, Nachiket P. Marathe
Summary: The aim of this study was to investigate the prevalence of antibiotic resistance in Klebsiella pneumoniae in Bergen city and its potential spread into the marine environment through treated sewage. Colistin resistance was observed in 35 out of 563 presumed K. pneumoniae isolates, while cefotaxime and tigecycline resistance were observed in only five isolates each. Clinically important acquired antibiotic resistance genes and virulence factors were detected in the sequenced Klebsiella spp. isolates. The study highlights the importance of sewage-based surveillance in understanding antibiotic resistance and provides a framework for population-based resistance surveillance in K. pneumoniae.
INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH
(2023)
Article
Multidisciplinary Sciences
Elisa Beninca, Susanne Pinto, Bernard Cazelles, Susana Fuentes, Sudarshan Shetty, Johannes A. Bogaards
Summary: Human microbiome research benefits from characterizing microbial networks, which can reveal key microbes for beneficial health effects. This study demonstrates the potential of wavelet clustering, a technique that clusters time series based on their spectral characteristics. The researchers apply this technique to densely sampled human gut microbiome time series and compare the results with traditional correlation-based methods, showing significant differences in terms of clustered elements, branching structure, and branch length. Wavelet clustering capitalizes on the dynamic nature of the human microbiome, revealing community structures that correlation-based methods may overlook.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Jolanda Kool, Liza Tymchenko, Sudarshan A. Shetty, Susana Fuentes
Summary: This study investigated the technical variations that can influence microbiota profiles in order to identify potential biases. By comparing multiple approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, the study revealed several important factors. The study emphasizes the importance of mechanical cell disruption and immediate frozen storage, and suggests considering differences in storage conditions in fecal microbiota studies.
FRONTIERS IN MICROBIOLOGY
(2023)
Letter
Infectious Diseases
Nachiket P. Marathe, Vera Radisic, Francisco Salva-Serra, Edward R. B. Moore, Didrik H. Grevskott
Review
Gastroenterology & Hepatology
Ziyu Huang, Yue Li, Heekuk Park, Martin Ho, Kanchan Bhardwaj, Naoki Sugimura, Hye Won Lee, Huicui Meng, Matthias P. Ebert, Kang Chao, Elke Burgermeister, Aadra P. Bhatt, Sudarshan A. Shetty, Kai Li, Weiping Wen, Tao Zuo
Summary: The urban population is growing globally, especially in developing Asian and African countries, leading to an increase in the burden of non-communicable diseases (NCDs). The gut microbiome plays a significant role in regulating the host's immune and metabolic homeostasis, linking external factors to host physiology. This review discusses the relationship between urbanization, dysbiosis of the gut microbiome, and the rising incidence of NCDs, as well as potential microbiome-inspired approaches to counteract NCDs.