Articles

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

Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish

Across taxa, animals with depleted intestinal microbiomes show disrupted behavioral phenotypes. Axenic (i.e., microbe-free) mice, zebrafish, and fruit flies exhibit increased locomotor behavior, or hyperactivi...

Authors: Chelsea A. Weitekamp, Allison Kvasnicka, Scott P. Keely, Nichole E. Brinkman, Xia Meng Howey, Shaza Gaballah, Drake Phelps, Tara Catron, Todd Zurlinden, Emily Wheaton and Tamara Tal

Inoculation with rumen fluid in early life accelerates the rumen microbial development and favours the weaning process in goats

Newborn ruminants possess an underdeveloped rumen which is colonized by microorganisms acquired from adult animals and the surrounding environment. This microbial transfer can be limited in dairy systems in wh...

Authors: Juan Manuel Palma-Hidalgo, Elisabeth Jiménez, Milka Popova, Diego Pablo Morgavi, Antonio Ignacio Martín-García, David Rafael Yáñez-Ruiz and Alejandro Belanche

Effects of aging on the skin and gill microbiota of farmed seabass and seabream

Important changes in microbial composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to r...

Authors: Daniela Rosado, Marcos Pérez-Losada, Ana Pereira, Ricardo Severino and Raquel Xavier

The porcine respiratory microbiome: recent insights and future challenges

Understanding the structure of the respiratory microbiome and its complex interactions with opportunistic pathogenic bacteria has become a topic of great scientific and economic interest in livestock productio...

Authors: Mattia Pirolo, Carmen Espinosa-Gongora, Debby Bogaert and Luca Guardabassi

Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon

Intestinal digesta is commonly used for studying responses of microbiota to dietary shifts, yet evidence is accumulating that it represents an incomplete view of the intestinal microbiota. The present work aim...

Authors: Yanxian Li, Leonardo Bruni, Alexander Jaramillo-Torres, Karina Gajardo, Trond M. Kortner and Åshild Krogdahl

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae

Aquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is just 2.5% of total market production. For cod farming to be a viable eco...

Authors: C. Keating, M. Bolton-Warberg, J. Hinchcliffe, R. Davies, S. Whelan, A. H. L. Wan, R. D. Fitzgerald, S. J. Davies, U. Z. Ijaz and C. J. Smith

The intestinal microbial composition in Greylag geese differs with steatosis induction mode: spontaneous or induced by overfeeding

Relationships between microbial composition and steatosis are being extensively studied in mammals, and causal relations have been evidenced. In migratory birds the liver can transiently store lipids during pr...

Authors: Christelle Knudsen, Julien Arroyo, Maxime Even, Laurent Cauquil, Géraldine Pascal, Xavier Fernandez, Franck Lavigne, Stéphane Davail, Sylvie Combes and Karine Ricaud

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

Oysters in coastal environments are subject to fluctuating environmental conditions that may impact the ecosystem services they provide. Oyster-associated microbiomes are responsible for some of these services...

Authors: Rebecca J. Stevick, Anton F. Post and Marta Gómez-Chiarri

Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons)

Herbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes. Recent research has found that captive management—an important conservation tool for many sp...

Authors: Raphael Eisenhofer, Kristofer M. Helgen and David Taggart

The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance

Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact ...

Authors: Bachar Cheaib, Hamza Seghouani, Martin Llewellyn, Katherine Vandal-Lenghan, Pierre-Luc Mercier and Nicolas Derome

Changes in the faecal microbiome of pied tamarins (Saguinus bicolor) associated with chronic, recurrent diarrhoea and weight loss

Chronic recurrent diarrhoea and weight loss is a common problem in captive callitrichids. These symptoms are common clinical features of marmoset wasting syndrome (MWS), a chronic enteric inflammation of unkno...

Authors: Peter Richards-Rios, Paul Wigley, Javier López, Dominic Wormell and Alberto Barbón

Oregano essential oil improves piglet health and performance through maternal feeding and is associated with changes in the gut microbiota

With a growing demand for safe and sustainable alternatives to antimicrobials, functional feed ingredients such as plant essential oils have been evaluated for their potential to improve gut health. Amongst th...

Authors: H. N. Hall, D. J. Wilkinson and M. Le Bon

Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counter...

Authors: Meredith K. Tavenner, Sue M. McDonnell and Amy S. Biddle

Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes

Impacts of biotic stressors, such as consumers, on coral microbiomes have gained attention as corals decline worldwide. Corallivore feeding can alter coral microbiomes in ways that contribute to dysbiosis, but...

Authors: Cody S. Clements, Andrew S. Burns, Frank J. Stewart and Mark E. Hay

Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides

Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographica...

Authors: Bianca R. P. Brown, Joaquin C. B. Nunez and David M. Rand

Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed compositio...

Authors: María Velasco-Galilea, Miriam Guivernau, Miriam Piles, Marc Viñas, Oriol Rafel, Armand Sánchez, Yuliaxis Ramayo-Caldas, Olga González-Rodríguez and Juan P. Sánchez

Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics

Host-specific microbiomes play an important role in individual health and ecology; in marine mammals, epidermal microbiomes may be a protective barrier between the host and its aqueous environment. Understandi...

Authors: Amy M. Van Cise, Paul R. Wade, Caroline E. C. Goertz, Kathy Burek-Huntington, Kim M. Parsons, Tonya Clauss, Roderick C. Hobbs and Amy Apprill

Bugs and drugs: a systems biology approach to characterising the effect of moxidectin on the horse’s faecal microbiome

Anthelmintic treatment is a risk factor for intestinal disease in the horse, known as colic. However the mechanisms involved in the onset of disease post anthelmintic treatment are unknown. The interaction bet...

Authors: S. P. Daniels, J. Leng, J. R. Swann and C. J. Proudman

Microbiomes of a specialist caterpillar are consistent across different habitats but also resemble the local soil microbial communities

Insect-associated microorganisms can provide a wide range of benefits to their host, but insect dependency on these microbes varies greatly. The origin and functionality of insect microbiomes is not well under...

Authors: Sofia I. F. Gomes, Anna M. Kielak, S. Emilia Hannula, Robin Heinen, Renske Jongen, Ivor Keesmaat, Jonathan R. De Long and T. Martijn Bezemer

Microbial co-occurrence networks of gut microbiota reveal community conservation and diet-associated shifts in cichlid fishes

The extent to which deterministic rather than stochastic processes guide gut bacteria co-existence and ultimately their assembling into a community remains largely unknown. Co-occurrence networks of bacterial ...

Authors: Joan Lluís Riera and Laura Baldo