Articles

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef

Coral reefs have sustained damage of increasing scale and frequency due to climate change, thereby intensifying the need to elucidate corals’ biological characteristics, including their thermal tolerance and m...

Authors: Leon Michael Hartman, Madeleine Josephine Henriette van Oppen and Linda Louise Blackall

Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in a...

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

Domesticated equine species and their derived hybrids differ in their fecal microbiota

Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the incr...

Authors: J. E. Edwards, A. Schennink, F. Burden, S. Long, D. A. van Doorn, W. F. Pellikaan, J. Dijkstra, E. Saccenti and H. Smidt

Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi

Next-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured. Here, we provide a metagenomic description of chemoautotrophic gammaproteobacterial sy...

Authors: Bonita McCuaig, Lourdes Peña-Castillo and Suzanne C. Dufour

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species

Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the w...

Authors: J. E. Edwards, S. A. Shetty, P. van den Berg, F. Burden, D. A. van Doorn, W. F. Pellikaan, J. Dijkstra and H. Smidt

Parrotfish predation drives distinct microbial communities in reef-building corals

Coral-associated microbial communities are sensitive to multiple environmental and biotic stressors that can lead to dysbiosis and mortality. Although the processes contributing to these microbial shifts remai...

Authors: Leïla Ezzat, Thomas Lamy, Rebecca L. Maher, Katrina S. Munsterman, Kaitlyn M. Landfield, Emily R. Schmeltzer, Cody S. Clements, Rebecca L. Vega Thurber and Deron E. Burkepile

Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome

As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we invest...

Authors: Younjung Kim, Marcus H. Y. Leung, Wendy Kwok, Guillaume Fournié, Jun Li, Patrick K. H. Lee and Dirk U. Pfeiffer

Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep

One of the greatest impediments to global small ruminant production is infection with the gastrointestinal parasite, Haemonchus contortus. In recent years there has been considerable interest in the gut microbiot...

Authors: Md. Abdullah Al Mamun, Mark Sandeman, Phil Rayment, Phillip Brook-Carter, Emily Scholes, Naga Kasinadhuni, David Piedrafita and Andrew R. Greenhill

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets

In pig production systems, weaning is a crucial period characterized by nutritional, environmental, and social stresses. Piglets transition from a milk-based diet to a solid, more complex plant-based diet, and...

Authors: Francesca Romana Massacci, Mustapha Berri, Gaetan Lemonnier, Elodie Guettier, Fany Blanc, Deborah Jardet, Marie Noelle Rossignol, Marie-José Mercat, Joël Doré, Patricia Lepage, Claire Rogel-Gaillard and Jordi Estellé

Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand

Scrub typhus, caused by a bacterial pathogen (Orientia spp.), is a potentially life-threatening febrile illness widely distributed in the Asia-Pacific region and is emerging elsewhere. The infection is transmitte...

Authors: Kittipong Chaisiri, A. Christina Gill, Alexandr A. Stekolnikov, Soawapak Hinjoy, John W. McGarry, Alistair C. Darby, Serge Morand and Benjamin L. Makepeace

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

The chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance...

Authors: Laura Glendinning, Kellie A. Watson and Mick Watson

Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements

Dietary intake is known to be a driver of microbial community dynamics in ruminants. Beef cattle go through a finishing phase that typically includes very high concentrate ratios in their feed, with consequent...

Authors: Timothy J. Snelling, Marc D. Auffret, Carol-Anne Duthie, Robert D. Stewart, Mick Watson, Richard J. Dewhurst, Rainer Roehe and Alan W. Walker

Occurrence and expression of genes encoding methyl-compound production in rumen bacteria

Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas...

Authors: William J. Kelly, Sinead C. Leahy, Janine Kamke, Priya Soni, Satoshi Koike, Roderick Mackie, Rekha Seshadri, Gregory M. Cook, Sergio E. Morales, Chris Greening and Graeme T. Attwood

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease ...

Authors: Anne Kauter, Lennard Epping, Torsten Semmler, Esther-Maria Antao, Dania Kannapin, Sabita D. Stoeckle, Heidrun Gehlen, Antina Lübke-Becker, Sebastian Günther, Lothar H. Wieler and Birgit Walther

Ecological specificity of the metagenome in a set of lower termite species supports contribution of the microbiome to adaptation of the host

Elucidating the interplay between hosts and their microbiomes in ecological adaptation has become a central theme in evolutionary biology. A textbook example of microbiome-mediated adaptation is the adaptation...

Authors: Lena Waidele, Judith Korb, Christian R. Voolstra, Franck Dedeine and Fabian Staubach

Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis

Clostridium perfringens is a key pathogen in poultry-associated necrotic enteritis (NE). To date there are limited Whole Genome Sequencing based studies describing broiler-associated C. perfringens in healthy and...

Authors: Raymond Kiu, Joseph Brown, Harley Bedwell, Charlotte Leclaire, Shabhonam Caim, Derek Pickard, Gordon Dougan, Ronald A. Dixon and Lindsay J. Hall

Looking like the locals - gut microbiome changes post-release in an endangered species

Captivity presents extreme lifestyle changes relative to the wild, and evidence of microbiome dysbiosis in captive animals is growing. The gut microbiome plays a crucial role in host health. Whilst captive bre...

Authors: Rowena Chong, Catherine E. Grueber, Samantha Fox, Phil Wise, Vanessa R. Barrs, Carolyn J. Hogg and Katherine Belov

Similar bacterial communities on healthy and injured skin of black tip reef sharks

Sharks are in severe global decline due to human exploitation. The additional concern of emerging diseases for this ancient group of fish, however, remains poorly understood. While wild-caught and captive shar...

Authors: Claudia Pogoreutz, Mauvis A. Gore, Gabriela Perna, Catriona Millar, Robert Nestler, Rupert F. Ormond, Christopher R. Clarke and Christian R. Voolstra

Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice

Growing evidence supports the role of gut microbiota in obesity and its related disorders including type 2 diabetes. Ob/ob mice, which are hyperphagic due to leptin deficiency, are commonly used models of obes...

Authors: Alireza Kashani, Asker Daniel Brejnrod, Chunyu Jin, Timo Kern, Andreas Nygaard Madsen, Louise Aas Holm, Georg K. Gerber, Jens-Christian Holm, Torben Hansen, Birgitte Holst and Manimozhiyan Arumugam

The microbiome of the invertebrate model host Galleria mellonella is dominated by Enterococcus

The popularity of Galleria mellonella as invertebrate model is increasing rapidly, because it forms an attractive alternative to study bacterial, fungal and viral infections, toxin biology, and to screen antimicr...

Authors: Camille Nina Allonsius, Wannes Van Beeck, Ilke De Boeck, Stijn Wittouck and Sarah Lebeer

Take care of the environment: housing conditions affect the interplay of nutritional interventions and intestinal microbiota in broiler chickens

The intestinal microbiota is shaped by many interactions between microorganisms, host, diet, and the environment. Exposure to microorganisms present in the environment, and exchange of microorganisms between h...

Authors: Jannigje G. Kers, Francisca C. Velkers, Egil A. J. Fischer, Gerben D. A. Hermes, David M. Lamot, J. Arjan Stegeman and Hauke Smidt

Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala

Differences between individuals in their gastrointestinal microbiomes can lead to variation in their ability to persist on particular diets. Koalas are dietary specialists, feeding almost exclusively on Eucalyptu...

Authors: Michaela D. J. Blyton, Rochelle M. Soo, Desley Whisson, Karen J. Marsh, Jack Pascoe, Mark Le Pla, William Foley, Philip Hugenholtz and Ben D. Moore

Impact of coccidiostat and phytase supplementation on gut microbiota composition and phytate degradation in broiler chickens

There is good evidence for a substantial endogenous phytase activity originating from the epithelial tissue or the microbiota resident in the digestive tract of broiler chickens. However, ionophore coccidiosta...

Authors: Susanne Künzel, Daniel Borda-Molina, Rebecca Kraft, Vera Sommerfeld, Imke Kühn, Amélia Camarinha-Silva and Markus Rodehutscord

Correction to: Effect of the macroalgae Asparagopsis taxiformis on methane production and rumen microbiome assemblage

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Authors: Breanna Michell Roque, Charles Garrett Brooke, Joshua Ladau, Tamsen Polley, Lyndsey Jean Marsh, Negeen Najafi, Pramod Pandey, Latika Singh, Robert Kinley, Joan King Salwen, Emiley Eloe-Fadrosh, Ermias Kebreab and Matthias Hess

Effect of the macroalgae Asparagopsis taxiformis on methane production and rumen microbiome assemblage

Recent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis has the potential to reduce methane (CH₄) production from beef cattle by up to ~ 99% when added to Rhodes grass hay;...

Authors: Breanna Michell Roque, Charles Garrett Brooke, Joshua Ladau, Tamsen Polley, Lyndsey Jean Marsh, Negeen Najafi, Pramod Pandey, Latika Singh, Robert Kinley, Joan King Salwen, Emiley Eloe-Fadrosh, Ermias Kebreab and Matthias Hess

Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore

Current knowledge about seasonal variation in the gut microbiota of vertebrates is limited to a few studies based on mammalian fecal samples. Seasonal changes in the microbiotas of functionally distinct gut re...

Authors: Sergei V. Drovetski, Michael J. V. O’Mahoney, Kenan O. Matterson, Brian K. Schmidt and Gary R. Graves

Welcome to Animal Microbiome

Authors: Sharon A. Huws