Articles

Effect of maternal separation and transportation stress on the bovine upper respiratory tract microbiome and the immune response to resident opportunistic pathogens

The bovine upper respiratory tract (URT) microbiome includes opportunistic pathogens that cause respiratory disease and stress associated with maternal separation and transportation contributes to the severity...

Authors: Nilusha Malmuthuge, Angela Howell, Natasa Arsic, Tracy Prysliak, Jose Perez-Casal and Philip Griebel

Elasmobranch microbiomes: emerging patterns and implications for host health and ecology

Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oc...

Authors: Cameron T. Perry, Zoe A. Pratte, Ana Clavere-Graciette, Kim B. Ritchie, Robert E. Hueter, Alisa L. Newton, G. Christopher Fischer, Elizabeth A. Dinsdale, Michael P. Doane, Krystan A. Wilkinson, Kim Bassos-Hull, Kady Lyons, Alistair D. M. Dove, Lisa A. Hoopes and Frank J. Stewart

High royal jelly production does not impact the gut microbiome of honey bees

Honey bees are not only essential for pollination services, but are also economically important as a source of hive products (e.g., honey, royal jelly, pollen, wax, and propolis) that are used as foods, cosmet...

Authors: Megan E. Damico, Olav Rueppell, Zack Shaffer, Bin Han and Kasie Raymann

Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta)

Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species ...

Authors: Klara Filek, Adriana Trotta, Romana Gračan, Antonio Di Bello, Marialaura Corrente and Sunčica Bosak

Temporal and nutritional effects on the weaner pig ileal microbiota

The porcine gastrointestinal microbiota has been linked to both host health and performance. Most pig gut microbiota studies target faecal material, which is not representative of microbiota dynamics in other ...

Authors: Jolinda Pollock, Laura Glendinning, Lesley A. Smith, Hamna Mohsin, David L. Gally, Michael R. Hutchings and Jos G. M. Houdijk

Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs

The role of the microbiome in livestock production has been highlighted in recent research. Currently, little is known about the microbiome's impact across different systems of production in swine, particularl...

Authors: Christian Maltecca, Rob Dunn, Yuqing He, Nathan P. McNulty, Constantino Schillebeeckx, Clint Schwab, Caleb Shull, Justin Fix and Francesco Tiezzi

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels

Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) are obligate hibernators and are only active 4–5 months annually. During this period, squirrels rapidly acquire fat for use during hibernation. We inve...

Authors: Kirsten Grond, Courtney C. Kurtz, Jasmine Hatton, Michelle M. Sonsalla and Khrystyne N. Duddleston

Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration

Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammon...

Authors: Aaron C. Ericsson, Susheel B. Busi, Daniel J. Davis, Henda Nabli, David C. Eckhoff, Rebecca A. Dorfmeyer, Giedre Turner, Payton S. Oswalt, Marcus J. Crim and Elizabeth C. Bryda

The link between broiler flock heterogeneity and cecal microbiome composition

Despite low genetic variation of broilers and deployment of considerate management practices, there still exists considerable body weight (BW) heterogeneity within broiler flocks which adversely affects the co...

Authors: Randi Lundberg, Christian Scharch and Dorthe Sandvang

A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing

Health surveillance of murine colonies employed for scientific purposes aim at detecting unwanted infection that can affect the well-being of animals and personnel, and potentially undermine scientific results...

Authors: Ferdinando Scavizzi, Cristian Bassi, Laura Lupini, Paola Guerriero, Marcello Raspa and Silvia Sabbioni

Environmentally enriched housing conditions affect pig welfare, immune system and gut microbiota in early life

Conventional pig housing and management conditions are associated with gastrointestinal pathophysiology and disease susceptibility in early life. Developing new strategies to reduce both therapeutic and prophy...

Authors: Caifang Wen, Ingrid van Dixhoorn, Dirkjan Schokker, Henri Woelders, Norbert Stockhofe-Zurwieden, Johanna M. J. Rebel and Hauke Smidt

The genetic diversity of “papillomavirome” in bovine teat papilloma lesions

Papillomaviruses are small nonenveloped, circular double-stranded DNA viruses that belong to the Papillomaviridae family. To date, 29 Bos taurus papillomavirus (BPV) types have been described. Studies involving m...

Authors: Jéssica Tatiane Sauthier, Cíntia Daudt, Flavio Roberto Chaves da Silva, Christian Diniz Beduschi Travassos Alves, Fabiana Quoos Mayer, Ronaldo Michel Bianchi, David Driemeier, Rodrigo Silva Araujo Streit, Charley Christian Staats, Cláudio Wageck Canal and Matheus Nunes Weber

Functional enrichment of gut microbiome by early supplementation of Bacillus based probiotic in cage free hens: a field study

The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. ...

Authors: Samiullah Khan and Kapil K. Chousalkar

Characterization of the gut microbiome in wild rocky mountainsnails (Oreohelix strigosa)

The Rocky Mountainsnail (Oreohelix strigosa) is a terrestrial gastropod of ecological importance in the Rocky Mountains of western United States and Canada. Across the animal kingdom, including in gastropods, gut...

Authors: Bridget Chalifour and Jingchun Li

Captivity reduces diversity and shifts composition of the Brown Kiwi microbiome

Captive rearing is often critical for animals that are vulnerable to extinction in the wild. However, few studies have investigated the extent to which captivity impacts hosts and their gut microbiota, despite...

Authors: Priscilla A. San Juan, Isabel Castro and Manpreet K. Dhami

Sustainable plant-based diets promote rainbow trout gut microbiota richness and do not alter resistance to bacterial infection

Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Altho...

Authors: David Pérez-Pascual, Ana Elena Pérez-Cobas, Dimitri Rigaudeau, Tatiana Rochat, Jean-François Bernardet, Sandrine Skiba-Cassy, Yann Marchand, Eric Duchaud and Jean-Marc Ghigo

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal

Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental chang...

Authors: Mason R. Stothart and Amy E. M. Newman

Metatranscriptomic analysis of colonic microbiota’s functional response to different dietary fibers in growing pigs

Dietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expr...

Authors: Jie Xu, Rongying Xu, Menglan Jia, Yong Su and Weiyun Zhu

Metagenomics analysis revealed the distinctive ruminal microbiome and resistive profiles in dairy buffaloes

Antimicrobial resistance poses super challenges in both human health and livestock production. Rumen microbiota is a large reservoir of antibiotic resistance genes (ARGs), which show significant varations in d...

Authors: Hui-Zeng Sun, Ke-Lan Peng, Ming-Yuan Xue and Jian-Xin Liu

Vertically transmitted microbiome protects eggs from fungal infection and egg failure

Beneficial microbes can be vertically transmitted from mother to offspring in many organisms. In oviparous animals, bacterial transfer to eggs may improve egg success by inhibiting fungal attachment and infect...

Authors: M. E. Bunker, G. Elliott, H. Heyer-Gray, M. O. Martin, A. E. Arnold and S. L. Weiss

Effect of sequentially fed high protein, hydrolyzed protein, and high fiber diets on the fecal microbiota of healthy dogs: a cross-over study

Dietary content and environmental factors can shape the gut microbiota, and consequently, the way the gut microbiota metabolizes fats, carbohydrates, and proteins, affecting overall health of the host. We eval...

Authors: Lina María Martínez-López, Amy Pepper, Rachel Pilla, Andrew P. Woodward, Jan S. Suchodolski and Caroline Mansfield

Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review

Undesirable microbial infiltration into the female bovine reproductive tracts, for example during calving or mating, is likely to disturb the commensal microflora. Persistent establishment and overgrowth of ce...

Authors: Chian Teng Ong, Conny Turni, Patrick J. Blackall, Gry Boe-Hansen, Ben J. Hayes and Ala E. Tabor

Correction to: Microbiota populations in supragingival plaque, subgingival plaque, and saliva habitats of adult dogs

Authors: Patrícia M. Oba, Meredith Q. Carroll, Celeste Alexander, Helen Valentine, Amy J. Somrak, Stephanie C. J. Keating, Adrianna M. Sage and Kelly S. Swanson

Gut microbiota of frugo-folivorous sifakas across environments

Captive animals, compared to their wild counterparts, generally harbor imbalanced gut microbiota owing, in part, to their altered diets. This imbalance is particularly striking for folivores that fundamentally...

Authors: Lydia K. Greene, Marina B. Blanco, Elodi Rambeloson, Karlis Graubics, Brian Fanelli, Rita R. Colwell and Christine M. Drea

Microbiota populations in supragingival plaque, subgingival plaque, and saliva habitats of adult dogs

Oral diseases are common in dogs, with microbiota playing a prominent role in the disease process. Oral cavity habitats harbor unique microbiota populations that have relevance to health and disease. Despite t...

Authors: Patrícia M. Oba, Meredith Q. Carroll, Celeste Alexander, Helen Valentine, Amy J. Somrak, Stephanie C. J. Keating, Adrianna M. Sage and Kelly S. Swanson

Perinatal exposure to tetracycline contributes to lasting developmental effects on offspring

For more than 30 years, the tetracycline on/off system of inducible gene expression has been leveraged to study disease mechanisms across many research areas, especially that of metabolism and neuroscience. Th...

Authors: Elizabeth M. Hill, Christopher D. Howard, Tracy L. Bale and Eldin Jašarević

The microbiota of healthy dogs demonstrates individualized responses to synbiotic supplementation in a randomized controlled trial

Probiotics have been demonstrated to ameliorate clinical signs of gastrointestinal diseases in dogs in various studies. However, the effect of probiotics in a healthy population, as well as factors contributin...

Authors: Jirayu Tanprasertsuk, Aashish R. Jha, Justin Shmalberg, Roshonda B. Jones, LeeAnn M. Perry, Heather Maughan and Ryan W. Honaker

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection

Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154^T ...

Authors: J. Le Luyer, Q. Schull, P. Auffret, P. Lopez, M. Crusot, C. Belliard, C. Basset, Q. Carradec, J. Poulain, S. Planes and D. Saulnier

MAP, Johne’s disease and the microbiome; current knowledge and future considerations

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne’s disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the ani...

Authors: Chloe Matthews, Paul D. Cotter and Jim O’ Mahony

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. He...

Authors: Connie A. Rojas, Santiago Ramírez-Barahona, Kay E. Holekamp and Kevin R. Theis

Metatranscriptomic analyses reveal ruminal pH regulates fiber degradation and fermentation by shifting the microbial community and gene expression of carbohydrate-active enzymes

Volatile fatty acids (VFA) generated from ruminal fermentation by microorganisms provide up to 75% of total metabolizable energy in ruminants. Ruminal pH is an important factor affecting the profile and produc...

Authors: Meng M. Li, Robin R. White, Le Luo Guan, Laura Harthan and Mark D. Hanigan

Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning

The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. Rumen microbiome analysis is often limited to invasive rumen ...

Authors: Nida Amin, Sarah Schwarzkopf, Asako Kinoshita, Johanna Tröscher-Mußotter, Sven Dänicke, Amélia Camarinha-Silva, Korinna Huber, Jana Frahm and Jana Seifert

Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals

Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut micr...

Authors: Davide Bozzi, Jacob A. Rasmussen, Christian Carøe, Harald Sveier, Kristian Nordøy, M. Thomas P. Gilbert and Morten T. Limborg

Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats

The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has...

Authors: Britton A. Strickland, Mira C. Patel, Meghan H. Shilts, Helen H. Boone, Arash Kamali, Wei Zhang, Daniel Stylos, Marina S. Boukhvalova, Christian Rosas-Salazar, Shibu Yooseph, Seesandra V. Rajagopala, Jorge C. G. Blanco and Suman R. Das

Peripheral blood mononuclear cells (PBMC) microbiome is not affected by colon microbiota in healthy goats

The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripher...

Authors: Ainize Peña-Cearra, Alejandro Belanche, Monika Gonzalez-Lopez, José Luis Lavín, Miguel Ángel Pascual-Itoiz, Elisabeth Jiménez, Héctor Rodríguez, Ana Mª. Aransay, Juan Anguita, David R. Yáñez-Ruiz and Leticia Abecia

Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation

The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of ...

Authors: Sandeep Kumar, M. Ajmal Khan, Emma Beijer, Jinxin Liu, Katherine K. Lowe, Wayne Young, David A. Mills and Christina D. Moon

Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry

Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may unde...

Authors: Ting-bei Bo and Kevin D. Kohl

Fish predation on corals promotes the dispersal of coral symbionts

The microbiomes of foundation (habitat-forming) species such as corals and sponges underpin the biodiversity, productivity, and stability of ecosystems. Consumers shape communities of foundation species throug...

Authors: Carsten G. B. Grupstra, Kristen M. Rabbitt, Lauren I. Howe-Kerr and Adrienne M. S. Correa

A diet-specific microbiota drives Salmonella Typhimurium to adapt its in vivo response to plant-derived substrates

Little is known about the complex interactions between the diet, the gut microbiota, and enteropathogens. Here, the impact of two specific diets on the composition of the mouse gut microbiota and on the transc...

Authors: Nicoletta Prax, Stefanie Wagner, Jakob Schardt, Klaus Neuhaus, Thomas Clavel and Thilo M. Fuchs

Effects of calcium level and source, formic acid, and phytase on phytate degradation and the microbiota in the digestive tract of broiler chickens

Diet acidification, dietary calcium (Ca) level, and phytase supplementation are known influences on the microbial community in the digestive tract and on phosphorus (P) utilization of broiler chickens. Effects of...

Authors: Jochen Krieg, Daniel Borda-Molina, Wolfgang Siegert, Vera Sommerfeld, Yung Ping Chi, Hamid Reza Taheri, Dieter Feuerstein, Amélia Camarinha-Silva and Markus Rodehutscord

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis

Clinical intervention during bacterial infections in farm animals such as pigs commonly includes the use of antimicrobials. With the rise of antimicrobial resistance and the attempts to reduce the use of antib...

Authors: Adrian Muwonge, Anbu K. Karuppannan and Tanja Opriessnig

Effect of copper sulfate on the external microbiota of adult common snook (Centropomus undecimalis)

The environment exerts a strong influence on the fish external microbiota, with lower diversity and increased abundances of opportunistic bacterial groups characterizing cultured fish compared to their wild co...

Authors: Andrea M. Tarnecki, Noah J. Levi, Matthew Resley and Kevan Main

Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets

Gut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals....

Authors: Kasun H. Bodawatta, Inga Freiberga, Katerina Puzejova, Katerina Sam, Michael Poulsen and Knud A. Jønsson

The dysbiosis of ovine foot microbiome during the development and treatment of contagious ovine digital dermatitis

Contagious Ovine Digital Dermatitis (CODD) is an emerging and common infectious foot disease of sheep which causes severe welfare and economic problems for the sheep industry. The aetiology of the disease is n...

Authors: J. S. Duncan, J. W. Angell, P. Richards, L. Lenzi, G. J. Staton, D. Grove-White, S. Clegg, G. Oikonomou, S. D. Carter and N. J. Evans

Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits

Antimicrobial resistance is one of the most urgent threat to global public health, as it can lead to high morbidity, mortality, and medical costs for humans and livestock animals. In ruminants, the rumen micro...

Authors: Ming-Yuan Xue, Yun-Yi Xie, Yi-Fan Zhong, Jian-Xin Liu, Le Luo Guan and Hui-Zeng Sun

The skin microbiome of Xenopus laevis and the effects of husbandry conditions

Historically the main source of laboratory Xenopus laevis was the environment. The increase in genetically altered animals and evolving governmental constraints around using wild-caught animals for research has l...

Authors: Maya Z. Piccinni, Joy E. M. Watts, Marie Fourny, Matt Guille and Samuel C. Robson

Longitudinal assessment of the bovine ocular bacterial community dynamics in calves

Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases of beef cattle. As such, IBK costs the US beef industry at least 150 million annually. However, ...

Authors: Alison C. Bartenslager, Nirosh D. Althuge, John Dustin Loy, Matthew M. Hille, Matthew L. Spangler and Samodha C. Fernando

Ceftiofur reduced Fusobacterium leading to uterine microbiota alteration in dairy cows with metritis

Metritis is an inflammatory uterine disease found in ~ 20% of dairy cows after parturition and associated with uterine microbiota with high abundance of Fusobacterium, Bacteroides, and Porphyromonas. Ceftiofur is...

Authors: Soo Jin Jeon, Federico Cunha, Rodolfo Daetz, Rodrigo C. Bicalho, Svetlana Lima and Klibs N. Galvão

Microbiota in intestinal digesta of Atlantic salmon (Salmo salar), observed from late freshwater stage until one year in seawater, and effects of functional ingredients: a case study from a commercial sized research site in the Arctic region

The importance of the gut microbiota for health and wellbeing is well established for humans and some land animals. The gut microbiota is supposedly as important for fish, but existing knowledge has many gaps,...

Authors: Jie Wang, Alexander Jaramillo-Torres, Yanxian Li, Trond M. Kortner, Karina Gajardo, Øyvind Jakobsen Brevik, Jan Vidar Jakobsen and Åshild Krogdahl

Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiolog...

Authors: Sesilje Weiss, David Taggart, Ian Smith, Kristofer M. Helgen and Raphael Eisenhofer