Article
Ecology
Dagmar Cizkova, Ludovit Dureje, Jaroslav Pialek, Jakub Kreisinger
Summary: Data on the gut microbiota of wild animals are crucial for studies in evolutionary biology, ecology, and conservation biology. A study on house mice found that sampling delay did not affect microbial composition, and that fecal microbiota can serve as a proxy for cecal microbiota, providing a non-invasive method for detecting biologically relevant patterns.
Article
Microbiology
Mengsha Li, Guanhua Dai, Liqiang Mu
Summary: Soil bacteria play important roles in mountain ecosystems, and changes in soil physicochemical properties are important factors shaping the diversity, composition, and function of soil bacteria.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Ying Wen, Gaosen Zhang, Wei Zhang, Guangxiu Liu
Summary: Deserts are extreme environments with multiple environmental stresses. Bacteria in desert ecosystems have diverse functions and play important roles.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Colin Buttimer, Francesca Bottacini, Andrey N. Shkoporov, Lorraine A. Draper, Paul Ross, Colin Hill
Summary: The study identified seven novel strains of Eggerthella lenta and conducted comparative and pangenome analyses to investigate the diversity of prophages associated with this species, revealing a complex relationship between the bacterium and diverse prophages.
Article
Biotechnology & Applied Microbiology
Richard Muirhead, Carina Schoensee
Summary: This study examined the survival, mobilization, and transport of Escherichia coli in sheep faeces over an extended period of time. The results showed a significant increase of E. coli in faeces, with peak concentrations observed between Day 2 to Day 30. The study also found a significant relationship between E. coli concentrations in faeces and in the runoff.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Chao Liu, Yang Li, Yun Chen, Xue-xin Chen, Jianhua Huang, Antonis Rokas, Xing-Xing Shen
Summary: As the most diverse group of animals, insects play a crucial role in ecosystems. Horizontal gene transfer (HGT) is the transfer of genetic material between species by non-reproductive means. Recent studies on the genomic data of hundreds of insect species have revealed numerous HGT events and provided insights into the functions of foreign genes. However, the extent and mechanisms of HGT in insects are still open questions.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
S. R. Wu, X. D. Chen, J. L. Li, Y. T. Yang, Z. H. Cui, J. H. Yao
Summary: Supplementation of starter feed and alfalfa hay significantly increased the growth performance of preweaning yaks. Starter feed supplementation led to increased inflammation-related indicators in calf plasma, while supplementation of both starter feed and alfalfa hay could reduce these indicators and promote the proliferation of beneficial bacteria in the caecum, improving immune homeostasis.
Article
Immunology
Qingli Zhang, Meng Wang, Xin Ma, Zhijie Li, Chenghui Jiang, Yangyang Pan, Qiaoying Zeng
Summary: The four LAB strains isolated from yak feces showed acid and bile tolerance, as well as other characteristics that suggest their potential to survive and colonize in the gastrointestinal tract, making them suitable for preventing and treating bacterial disease-related diarrhea in yaks.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Brett A. Tortelli, Amanda L. Lewis, Justin C. Fay
Summary: The diversity and structure of vaginal strains vary across species, with Lactobacillus species showing lower strain diversity. The frequency of multi-strain samples is related to species-level diversity, indicating similar ecological factors influencing diversity within the vaginal niche. The structure of strain-level variation provides a means of testing whether strain-level differences contribute to the function and health consequences of the vaginal microbiome.
MICROBIAL GENOMICS
(2021)
Article
Agriculture, Dairy & Animal Science
Sara Muhonen, Sophie Sadet-Bourgeteau, Veronique Julliand
Summary: Horses are herbivores and benefit from diets rich in forage compared to concentrate. This study compared the effects of different forage diets on hindgut microorganisms and found no significant differences in microbial concentrations. Further research on plant-fibre and forage diets is important for horse feeding practices.
Article
Ecology
Stilianos Fodelianakis, Alex D. Washburne, Massimo Bourquin, Paraskevi Pramateftaki, Tyler J. Kohler, Michail Styllas, Matteo Tolosano, Vincent De Staercke, Martina Schoen, Susheel Bhanu Busi, Jade Brandani, Paul Wilmes, Hannes Peter, Tom J. Battin
Summary: Glacier-fed streams (GFSs) are extreme and rapidly disappearing ecosystems that harbor diverse microbial communities. A novel analytical framework called phyloscore analysis identified clades with lower spatial phylogenetic turnover in sediment microbiomes across twenty GFSs in New Zealand. These clades, constituting up to 44% and 64% of community alpha-diversity and abundance, showed increased alpha-diversity and abundance as sediment chlorophyll a decreased, indicating their ecological success in GFS habitats.
Article
Multidisciplinary Sciences
Manuel Delgado-Baquerizo, David J. Eldridge, Yu-Rong Liu, Blessing Sokoya, Jun-Tao Wang, Hang-Wei Hu, Ji-Zheng He, Felipe Bastida, Jose L. Moreno, Adebola R. Bamigboye, Jose L. Blanco-Pastor, Concha Cano-Diaz, Javier G. Illan, Thulani P. Makhalanyane, Christina Siebe, Pankaj Trivedi, Eli Zaady, Jay Prakash Verma, Ling Wang, Jianyong Wang, Tine Grebenc, Gabriel F. Penaloza-Bojaca, Tina U. Nahberger, Alberto L. Teixido, Xin-Quan Zhou, Miguel Berdugo, Jorge Duran, Alexandra Rodriguez, Xiaobing Zhou, Fernando Alfaro, Sebastian Abades, Cesar Plaza, Ana Rey, Brajesh K. Singh, Leho Tedersoo, Noah Fierer
Summary: The structure and function of soil microbiomes in urban greenspaces are largely uniform worldwide. Urban soils contain a higher proportion of fast-growing microbes and lower levels of ectomycorrhizal fungi compared to natural ecosystems. City affluence, management practices, and climate are key factors influencing urban soil communities.
Review
Multidisciplinary Sciences
M. McCauley, T. L. Goulet, C. R. Jackson, S. Loesgen
Summary: Microorganisms are crucial for the health and resilience of cnidarians. However, comparing cnidarian microbiomes across studies is challenging due to the variety of protocols used. In this study, researchers analyzed 12,010 cnidarian microbiome samples, along with samples from other organisms, to identify the factors influencing cnidarian microbiomes. They found a wide diversity of archaeal and bacterial phyla associated with cnidarians and identified key bacteria influenced by host characteristics, sampling depth, and ocean location. This systematic review provides a framework for understanding cnidarian microbiomes and their response to stress.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Yang Yu, Lu Liu, Jing Wang, Yushu Zhang, Chunwang Xiao
Summary: The study shows that warming increases the α-diversity of soil bacteria, enhances network complexity and stability, and promotes the development of keystone taxa. Additionally, warming also increases the ability of bacteria to decompose organic matter and emit greenhouse gases.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Microbiology
Haiping Ni, Rui Zong, Jianjun Sun, Yuxia Wu, Lei Yu, Yuanyuan Liu, Jin Liu, Ruicheng Ju, Xianli Sun, Yulian Zheng, Lekun Tan, Lumin Liu, Yachao Dong, Tao Li, Youming Zhang, Qiang Tu
Summary: This study examines the bacterial community in the soil-root system of different severity of clubroot disease. It identifies the composition and structure of soil bacteria and potential biomarkers of the disease. The study also highlights the importance of pH in the abundance of specific bacteria and provides insights for the monitoring and biocontrol of clubroot disease in Chinese cabbage.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Martin Beaumont, Laurent Cauquil, Allan Bertide, Ingrid Ahn, Celine Barilly, Lisa Gil, Cecile Canlet, Olivier Zemb, Geraldine Pascal, Arnaud Samson, Sylvie Combes
Summary: The gut microbiota produces different metabolites in suckling and weaned piglets, including short-chain fatty acids and biogenic amines. The origin of the piglets also impacts the levels of certain bacterial metabolites. The fecal metabolome signatures in suckling and weaned piglets are associated with specific microbiota-predicted functionalities, structure, and diversity.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Agriculture, Dairy & Animal Science
Melanie Martignon, Christine Burel, Laurent Cauquil, Sylvie Combes, Thierry Gidenne
Summary: The study shows that feed restriction can improve rabbit growth performance and nutrient digestibility, while fragmented feed distribution does not have a significant impact on rabbit digestive health.
Article
Nutrition & Dietetics
Etienne Labussiere, Caroline Achard, Serge Dubois, Sylvie Combes, Mathieu Castex, David Renaudeau
Summary: Supplementing live yeast can improve feed intake, energy retention, and attenuate the effects of HS on fecal microbiota composition in finishing boars.
BRITISH JOURNAL OF NUTRITION
(2022)
Review
Agriculture, Dairy & Animal Science
A. Cabiddu, G. Peratoner, B. Valenti, V. Monteils, B. Martin, M. Coppa
Summary: Research in the last decades has shown that feeding management practices play a major role in improving the quality of ruminant products. However, most of the studies have been conducted under controlled conditions and have not been validated on-farm. This quantitative review examines the effects of on-farm feeding management practices on various quality traits of dairy products and meat. The results show that feeding fresh herbage and avoiding silage can increase the concentration of beneficial nutrients and fatty acids in ruminant products, while feeding animals from PSM-rich permanent grasslands can improve the fatty acid composition of dairy products. However, the differences observed under on-farm conditions are smaller than those observed in controlled trials.
Article
Nutrition & Dietetics
Martin Beaumont, Eloise Mussard, Celine Barilly, Corinne Lencina, Laure Gress, Louise Painteaux, Beatrice Gabinaud, Laurent Cauquil, Patrick Aymard, Cecile Canlet, Charlotte Paes, Christelle Knudsen, Sylvie Combes
Summary: This study found that in rabbits, the maturation of the gut microbiota at the suckling-to-weaning transition is primarily driven by the introduction of solid food, while the maturation of the intestinal epithelium is influenced by the developmental stage, solid food introduction, and suckling cessation.
JOURNAL OF NUTRITION
(2022)
Article
Biotechnology & Applied Microbiology
Marion Allaoua, Elsa Bonnafe, Pierre Etienne, Virginie Noirot, Jean-Francois Gabarrou, Adrien Castinel, Geraldine Pascal, Vincent Darbot, Michel Treilhou, Sylvie Combes
Summary: This study aimed to test the effectiveness of a carvacrol-based formulation in reducing C. jejuni load in broiler chickens and to study the impact of C. jejuni inoculation alone or combined with the product on the caecal microbiota. The results showed that the carvacrol-based product significantly decreased the C. jejuni load and that the combination of C. jejuni inoculation and the product increased the diversity and altered the structure of the microbial community.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Food Science & Technology
Julien Soulat, Brigitte Picard, Cecile Bord, Valerie Monteils
Summary: The aim of this study was to investigate the effects of rearing management on carcass and meat properties. The results showed that different rearing managements could achieve the same quality of carcass or meat. Management 3 was found to be an interesting trade-off for managing both carcass and LM meat quality.
Article
Multidisciplinary Sciences
Valerie Monteils, Cecile Sibra
Summary: This paper presents data on rearing practices collected from 45 beef heifer breeders, focusing on the different stages of the animals' life. The study examines various factors involved in the rearing practices and collects parameters from the carcasses produced.
Article
Agriculture, Dairy & Animal Science
Nathalie Le Floc'h, Caroline Stephanie Achard, Francis Amann Eugenio, Emmanuelle Apper, Sylvie Combes, Helene Quesnel
Summary: Feeding sows with live yeast Saccharomyces cerevisiae var. boulardii (SB) can influence the fecal microbiota of sows and their piglets, but does not have an effect on their health and performance.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Microbiology
Charlotte Paes, Thierry Gidenne, Karine Bebin, Joel Duperray, Charly Gohier, Emeline Guene-Grand, Gwenael Rebours, Celine Barilly, Beatrice Gabinaud, Laurent Cauquil, Adrien Castinel, Geraldine Pascal, Vincent Darbot, Patrick Aymard, Anne-Marie Debrusse, Martin Beaumont, Sylvie Combes
Summary: This study in a rabbit model showed that early introduction of solid food can accelerate gut microbiota maturation, and plant polysaccharides ingestion has a significant impact on the cecal microbiota.
Article
Cell Biology
Eloise Mussard, Corinne Lencina, Lise Gallo, Celine Barilly, Maryse Poli, Katia Feve, Mikael Albin, Laurent Cauquil, Christelle Knudsen, Caroline Achard, Guillaume Devailly, Laura Soler, Sylvie Combes, Martin Beaumont
Summary: Intestinal organoids generated from piglets retained a location-specific phenotype but not a developmental stage-specific phenotype. The luminal environment of the organoids was not representative of the in vivo environment, suggesting that reproducing the luminal environment might improve the physiological relevance of intestinal organoids.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Food Science & Technology
Julien Soulat, Valerie Monteils, Brigitte Picard
Summary: This study aimed to investigate the effects of rearing management on carcass and meat quality in young bulls. Five rearing managements were defined based on 30 rearing factors, and their impacts were analyzed on carcass traits (fat, overall meat grain) and meat traits (color, tenderness). It was found that different rearing managements could produce similar carcass and meat properties, with two management strategies identified as the best trade-off for high quality.
Article
Food Science & Technology
Julien Soulat, Brigitte Picard, Valerie Monteils
Summary: The study found that rearing managements have low effects on the carcass and meat properties of cull cows, with only a few specific traits being impacted. Trade-offs are needed to manage both carcass and meat qualities.
Article
Biochemistry & Molecular Biology
Martin Beaumont, Corinne Lencina, Katia Feve, Celine Barilly, Laurence Le-Normand, Sylvie Combes, Guillaume Devailly, Gaelle Boudry
Summary: The disruption of the primocolonizing gut microbiota alters epithelial innate immunity in the colon and imprints stem cells, which could have long-term consequences for gut health. Colistin, an antibiotic, was used in a newborn piglet model to deplete specific gram-negative bacteria in the neonatal gut microbiota. The depletion of these bacteria resulted in altered gene expression in the colon epithelium, decreased toll-like receptor 4 (TLR4) and lysozyme (LYZ) levels, and an increased concentration of succinate in the colon.
Article
Microbiology
Martin Beaumont, Corinne Lencina, Allan Bertide, Lise Gallo, Celine Barilly, Christelle Marrauld, Laurent Cauquil, Arnaud Samson, Sylvie Combes
Summary: This study suggests that the gut microbiota during the suckling period is not a major factor underlying the susceptibility of piglets to post-weaning diarrhea (PWD).
MICROBIOLOGY SPECTRUM
(2023)