Tag Archives: microbiome

Pets’ impact on human gut microbiome to be explored

Posted on December 30, 2021 | Leave a comment

Could pets offer “probiotic” benefits to their owners?

Researchers at the University of Pennsylvania School of Veterinary Medicine (Penn Vet) are set to investigate whether pets could be a source of microbiota that can help restore deficiencies in their owner’s gut microbiome (i.e. collection of microbes in the intestines).

The study, which has received funding from the Human Animal Bond Research Institute (HABRI), will follow pet owners (60 years or older) who are taking antibiotics for dental implant placement. Antibiotics disrupt the native gut microbiome, HABRI reports, which can result in adverse outcomes, ranging from mild diarrhea to severe “C. diff” (Clostridioides difficile) infection.

Researchers hypothesize the gut microbiomes of owners and their pets will resemble each other prior to the course of antibiotics, diverge during the disruption phase, then steadily converge during the recovery phase.

“A growing number of studies have documented the ability of animal contact to impact the human microbiome in ways that may help prevent certain types of disease, such as cardiovascular disease and asthma,” says principal investigator, Laurel Redding, VMD, PhD, DACVPM, an assistant professor of epidemiology at Penn Vet. “In conducting this study, our goal is to shed light on the microbial exchanges that occur between pets and pet owners and assess whether pets can mitigate disruption of their owner’s gut microbiome following antibiotic therapy.”

Researchers say the study’s results could support the promotion of contact between older adults and household pets, HABRI reports.

“HABRI is proud to fund research that will contribute to our understanding of the physiological health benefits of the human-animal bond,” says the group’s president, Steven Feldman. “We know pets and people are good for each other, and it’s exciting we can still discover new evidence underlying this powerful, mutually-beneficial relationship.”

Source: Veterinary Practice News

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The origin of feces (aka shit happens)

Posted on April 20, 2020 | 2 comments

The archaeological record is littered with feces, a potential goldmine for insights into ancient health and diet, parasite evolution, and the ecology and evolution of the microbiome. The main problem for researchers is determining whose feces is under examination. A recent study published in the journal PeerJ, led by Maxime Borry and Christina Warinner of Max Planck Institute for the Science of Human History (MPI-SHH), presents “CoproID: a reliable method of inferring sources of paleofeces.”

After thousands of years, the source of a particular piece of feces can be difficult to determine. Distinguishing human and dog feces is particularly difficult: they are similar in size and shape, occur at the same archaeological sites, and have similar compositions. In addition, dogs were on the menu for many ancient societies, and our canine friends have a tendency to scavenge on human feces, thus making simple genetic tests problematic, as such analyses can return DNA from both species.

Shit happens

H35 (Ash pit number 35) coprolites from Xiaosungang archaeological site, Anhui Province, China © Jada Ko, Courtesy of the Anhui Provincial Institute of Cultural Relics and Archaeology

In order to access the insights contained within paleofeces, the researchers developed coproID (coprolite identification). The method combines analysis of ancient host DNA with a machine learning software trained on the microbiomes within modern feces. Applying coproID to both newly sequenced and previously published datasets, the team of researchers from the MPI-SHH, Harvard University, and the University of Oklahoma were able to reliably predict the sources of ancient feces, showing that a combination of host DNA and the distinct colonies of microbes living inside humans and dogs allow their feces to be accurately distinguished.

Classification capability provides insights into digestive health

“One unexpected finding of our study is the realization that the archaeological record is full of dog poop,” says Professor Christina Warinner, senior author of the study. But Warinner also expects coproID to have broader applications, especially in the fields of forensics, ecology, and microbiome sciences.

The ability to accurately identify the source of archaeological feces enables the direct investigation of changes in the structure and function of the human gut microbiome throughout time, which researchers hope will provide insights into food intolerances and a host of other issues in human health. “Identifying human coprolites should be the first step for ancient human microbiome analysis,” says the study’s first author, Maxime Borry.

“With additional data about the gut metagenomes of non-Westernized rural dogs, we’ll be better able to classify even more ancient dog feces as in fact being canine, as opposed to ‘uncertain,’” Borry adds. As the catalog of human and dog microbiome data grows, coproID will continue to improve its classifications and better aid researchers that encounter paleofeces in a range of geographic and historical contexts.

Source:  Max Planck Institute for the Science of Human History

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Dog pee on the sidewalk does more than just piss off your neighbors

Posted on May 18, 2019 | Leave a comment

Note from DoggyMom:  I follow all types of research.  But some – like this one – needs to be put into a larger context.  Urban cities have a lot of runoff thanks to all the hard surfaces including roads and sidewalks.  Urban designers look to institute green spaces to help with infiltration of water into soils and decrease runoff, which can be particularly helpful in high volume, storm events which overwhelm stormwater systems.

Urban runoff has a lot of contaminants from the oils, dust and debris of modern life.  All meat-eating animals have high nitrogen in their urine – and that’s why countries like NZ have issues with groundwater quality because of the number of cows that are left to graze and urinate on open pastures.  So of course dogs will have an impact on the soil quality and runoff in the very limited areas of green that they have to use in urban cities.  The solution?  Well, in my opinion, it’s partly an argument for creating more green space.

Nobody knows just how many dogs there are in the United States, but there are plenty—and many of them live (and pee) in human cities. Turns out, canine bathroom breaks may have more of an impact on the environment than you might think.

In a new study, a team of Columbia University undergraduate and graduate researchers led by ecologist Krista McGuire looked at the impact of pee on the urban soil microbiome. They found evidence that the nitrogen content and low pH of the urine can make city soil both harder and less absorbent of rainwater, while making the soil microbiome less diverse.

Your very good boy

The project was born out of McGuire’s observations with colleagues during other research on green infrastructure in NYC. In sites like unfenced tree pits, “the soils seemed barren, compacted, and the water from rainfall didn’t seem to penetrate very well,” she says.

The team suspected soil’s characteristics had something to do with all the dogs that urinated on those sites, so they designed an experiment to check. “We obtained soil from the city environment,” says McGuire, along with one species of commonly-used plant from the same nursery the city uses.

Both of these factors replicate what’s used out in the real world. Getting actual dog pee turned out to be harder. They approached animal shelters, which mostly turned them away, while the one shelter that acquiesced didn’t yield enough pee—the experiment required a whopping 40 gallons.

“Despite visiting the shelter twice a week for a couple months, less than 40mL [1.35 oz] of urine was collected due to difficulty in predicting when the dogs will urinate and the dogs’ refusal to continue urinating when a collecting bowl was brought near them as they were about to urinate,” the paper states.

“Ultimately, we decided to use coyote urine since coyotes are very closely related to domestic dogs, and their urine is commercially available,” McGuire says. If you’re not a gardener looking to repel deer from your tulips, you may not be aware of this, but yes, you can buy 40 gallons of coyote pee pretty easily.  (Note from DoggyMom:  Coyotes are kept in captivity and their urine is collected through drainage systems.  Some say that the income from the coyote urine farms help to support other conservation efforts.   I will need to research this further.)

Over the course of a month, they ran a greenhouse experiment, watering the plants at regular intervals with either straight water or water mixed with urine at different concentrations. They checked the soil each week. The results were dramatic: the bacterial community diversity decreased by up to a third during the experiment, and the kinds of bacteria in the microbiome changed. Meanwhile, the “runoff” from pots increased significantly, signifying that the soil was becoming less absorbent.

Outside the lab (say, outside your door), “a variety of different events can affect the impact of urine deposition,” says Gary King, a Louisiana State University biology professor who studies urban microbiomes. This experiment doesn’t address those factors—like, what if it’s raining, or what if some other pollutant has recently entered the soil?

But the results point to an important direction of research, he says. “There is a huge gap in our knowledge about basic microbial functions in the soils that are part of the system in our own built environment.”

That’s a serious problem, because soils help keep a city running. Things like street trees and planted medians aren’t just there to make downtown look good. Cities are mostly built on hard surfaces like concrete and asphalt, which don’t absorb water and allow it to enter the soil, so the sewer system works to keep water off the roads and out of your basement. But sometimes, it rains too much for this system. That’s where what’s known as “green infrastructure” comes in, by helping to absorb all the extra water. Otherwise, says McGuire, “What happens is that the stormwater combines with raw sewage in these below-ground piping systems. Past a certain threshold, it gets spewed out into local waterways.”

To keep this from happening, cities like New York are investing lots of money in building and maintaining green infrastructure, from street trees to deliberately designed water capture landscapes called “bioswales.” But as this research indicates, our furry friends’ bathroom breaks may be making these interventions less effective.

Journal citation:  Evaluating the effects of canine urine on urban soil microbial communities

Source:   Popular Science

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Fresh and raw diets for dogs may have health benefits

Posted on August 25, 2018 | Leave a comment

Many dog owners think of their furry companions as part of the family, and now products are available to feed them that way, too. Some owners are moving away from traditional extruded kibble products, instead choosing ultra-premium fresh and raw diets found in the refrigerated aisle. The foods may look more similar to what we’d feed a member of the family, but many of the newer diets haven’t been rigorously tested for performance in dogs.

Beagle feeding study

“A lot of companies test for complete and balanced nutrition, but don’t go beyond that,” says Kelly Swanson, corresponding author on a new study published in the Journal of Animal Science and Kraft Heinz Company Endowed Professor in Human Nutrition in the Department of Animal Sciences and the Division of Nutritional Sciences at the University of Illinois. “The company we worked with – Freshpet – wanted to see how some of their unique diets would perform. Would dogs like them? Were they digestible? Would they increase activity?”

The researchers tested the palatability and digestibility of three commercially marketed fresh and raw diets for dogs, as well as a traditional extruded kibble diet. The diets included a lightly cooked roasted-refrigerated diet; a lightly cooked grain-free roasted-refrigerated diet; and a raw diet. The lightly cooked roasted diets were pasteurized, and the raw diet was treated with an acidifying bacteria that makes the food inhospitable to harmful microbes.

“The roasted diets come in a meatball form, and the raw diet was more like a big sausage roll that you cut up and feed to the dog. All diets were chicken-based, but some had added beef, salmon, or chicken liver. Each diet also contained a vitamin and mineral mix, and a dry mix of plant products like sweet potatoes, kale, spinach, cranberries, and carrots,” Swanson says. “People are familiar with those ingredients so they like to see them included in their pets’ diets. Although specific ingredients are not needed in the diet of dogs and cats, as many options can result in an acceptable nutrient profile, those ingredients are of high quality and are nutrient dense.”

Eight beagles were successively fed each diet for one month. After a 14-day transition period onto each new diet, they were monitored for voluntary physical activity, and then urine, stool, and blood samples were collected and analyzed.

The roasted diets turned out to be more digestible than the kibble, and both the grain-free roasted diet and the raw diet resulted in lower blood triglyceride levels than the kibble diet, even though they were higher in fat. Swanson isn’t able to pinpoint the cause of the surprising result, but points to it as a potential benefit of the non-traditional diets. Voluntary activity didn’t differ across the diets.

The researchers also found major shifts in the microbiota – the suite of microbes inhabiting the gut – in the roasted and raw diets, compared with kibble. Swanson says the changes in the microbiota were neither good nor bad, just different. He suggests that the results showcase the flexibility of gut microbiota, and how little scientists know about the effects of diet on host-microbe relationships as a whole.

It is important to point out that all dogs were healthy throughout the study period, and that all diets were palatable, highly digestible, and resulted in good stool quality. Even though some of the diets were statistically more digestible or led to lower triglycerides, those metrics were within the normal range for all dogs on all diets. Therefore, Swanson emphasizes, all the diet formats tested in the study, including kibble, would be healthy choices.

“As far as diet format and market segment is concerned, it ultimately comes down to consumer preference and philosophy. As long as a diet is shown to be safe and meets the nutritional needs of the pet in question, it is an acceptable option to me. If an owner is willing to pay more for premium ingredients and/or an improved processing method, I am fully supportive. To me, the most important thing is testing these new diet formats and products before they are commercially available,” Swanson says.

The article, “Apparent total-tract macronutrient digestibility, serum chemistry, urinalysis, and fecal characteristics, metabolites and microbiota of adult dogs fed extruded, mildly cooked, and raw diets,” is published in the Journal of Animal Science [DOI: 10.1093/jas/sky235]. Authors include Kiley Algya, Tzu-Wen Cross, Kristen Leuck, Megan Kastner, Toshiro Baba, Lynn Lye, Maria de Godoy, and Kelly Swanson. Lynn Lye is from Freshpet, and all other authors are from U of I. The research was funded by Freshpet.

Source:  University of Illinois press release

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Dogs could be more similar to humans than we thought

Posted on April 23, 2018 | Leave a comment

Dog and human gut microbiomes have more similar genes and responses to diet than we previously thought, according to a study published in the open access journal, Microbiome.

Canine Microbiome

The canine microbiome is quite similar to that of humans. Credit: © Kar Tr / Fotolia

Dr Luis Pedro Coelho and colleagues from the European Molecular Biology Laboratory, in collaboration with Nestlé Research, evaluated the gut microbiome of two dog breeds and found that the gene content of the dogs microbiome showed many similarities to the human gut microbiome, and was more similar to humans than the microbiome of pigs or mice.

Dr Luis Pedro Coelho, corresponding author of the study, commented: “We found many similarities between the gene content of the human and dog gut microbiomes. The results of this comparison suggest that we are more similar to man’s best friend than we originally thought.”

The researchers found that changes in the amount of protein and carbohydrates in the diet had a similar effect on the microbiota of dogs and humans, independent of the dog’s breed or sex. The microbiomes of overweight or obese dogs were found to be more responsive to a high protein diet compared to microbiomes of lean dogs; this is consistent with the idea that healthy microbiomes are more resilient.

Dr Luis Pedro Coelho, commented: “These findings suggest that dogs could be a better model for nutrition studies than pigs or mice and we could potentially use data from dogs to study the impact of diet on gut microbiota in humans, and humans could be a good model to study the nutrition of dogs.

“Many people who have pets consider them as part of the family and like humans, dogs have a growing obesity problem. Therefore, it is important to study the implications of different diets.”

The researchers investigated how diet interacted with the dog gut microbiome with a randomized controlled trial using a sample of 64 dogs, half of which were beagles and half were retrievers, with equal numbers of lean and overweight dogs. The dogs were all fed the same base diet of commercially available dog food for four weeks then they were randomized into two groups; one group consumed a high protein, low carb diet and the other group consumed a high carb, low protein diet for four weeks. A total of 129 dog stool samples were collected at four and eight weeks. The researchers then extracted DNA from these samples to create the dog gut microbiome gene catalogue containing 1,247,405 genes. The dog gut gene catalogue was compared to existing gut microbiome gene catalogues from humans, mice and pigs to assess the similarities in gene content and how the gut microbiome responds to changes in diet.

The authors caution that while humans and dogs host very similar microbes, they are not exactly the same microbes, but very closely related strains of the same species.

Source:  Science Daily

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Study Shows How a Dog’s Diet Shapes Its Gut Microbiome

Posted on January 26, 2017 | Leave a comment

Studies of the gut microbiome have gone to the dogs — and pets around the world could benefit as a result.

In a  paper published in the journal mBio, researchers from Nestle Purina PetCare Company report that the ratio of proteins and carbohydrates in a canine’s daily diet have a significant influence on the balance of microbes in its gut. Among other findings, they observed that dogs fed a high-protein, low-carbohydrate diet had decreases in the ratio of Bacteroidetes to Firmicutes bacteria, as well as enriched microbial gene networks associated with weight loss in humans. The microbial responses were more pronounced in obese and overweight dogs than in dogs of a healthy weight.

microbiome-dog

The researchers say their study may help identify new microbiology-inspired strategies for managing pet obesity, which is  a growing problem. More than half of pet dogs in the United States are overweight or obese, according to the most recent annual survey by the Association for Pet Obesity Prevention. A comparison of that data with previous surveys suggests that obesity in dogs, as in people, is getting worse.

“We do believe dogs have become heavier over the last decade, and that it’s an epidemic,” says Johnny Li, a computational biologist at Nestle Purina, in St. Louis, Missouri, who led the new study. Li says he launched the study because only a handful of previous studies have explored the gut microbiome of canines, and the effect of diet on gut microbes hasn’t been well documented.

Studies on animals are lacking, but human studies have connected microbial imbalance in the gut to a variety of conditions, including obesity, metabolic syndrome, cardiovascular disease, immune disorders, and liver and brain diseases.

Li and his team studied 32 Labrador Retrievers and 32 Beagles, with equal numbers of lean and overweight or obese dogs. During the first four weeks, all the dogs were fed the same baseline diet. During the second four weeks, half the dogs received a high-protein, low-carbohydrate diet; the other half received a high-carbohydrate, low-protein diet.

Fecal microbiome studies conducted after the first four weeks revealed few differences in the gut microbiomes of the dogs. Studies conducted after the second four weeks, after the dogs had eaten an experimental diet, showed dramatic changes in the microbiome. Dogs that ate a low-protein, high-carbohydrate diet had higher abundances of Bacteroides uniformis and Clostridium butyricum.

In dogs that ate a high-protein, low-carbohydrate diet, the researchers observed a decrease in the ratio of Bacteroidetes to Firmicutes bacteria. They also reported that abundances of Clostridium hiranonis, Clostridium perfringens, and Ruminococcus gnavus were more than double the abundances observed in the other experimental group.

Li says the effects of diet on the microbiome were more pronounced in obese and overweight dogs than in lean dogs. “That seems to suggest that obese dogs and overweight dogs are more susceptible to dietary intervention,” he says. A different diet for those animals may have a greater impact on the bacterial balance in their guts.

The study involved only two breeds, but Li says the findings are likely applicable to all dog breeds, “though we need more studies on other breeds in the future to be sure.”

Li says his team’s study provides a framework to explore the connection between diet and gut microbes in dogs. Although the findings are preliminary, he says he hopes to see the research eventually translate into real-world ways to modify pet food, perhaps through the strategic use of probiotics or prebiotics, and reduce the obesity epidemic.

View the paper Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions

Source:  American Society of Microbiology press release

 

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Changes in Skin “Microbiome” During Canine Atopic Dermatitis Could Lead to Antibiotic-Free Therapies

Posted on September 13, 2016 | Leave a comment

Atopic dermatitis (AD), a chronic inflammatory skin condition and the most common form of eczema, is estimated to afflict as much as 10 percent of the U.S. population, and is much more common now than it was 50 years ago. Veterinary clinical estimates also show that approximately 10 percent of dogs have atopic dermatitis.

How AD arises isn’t yet fully understood, but a study from researchers from the Perelman School of Medicine at the University of Pennsylvania and Penn’s School of Veterinary Medicine, have uncovered important insights about the association of AD in dogs compared to humans. The study appears online in the Journal of Investigative Dermatology.

atopy

To a greater extent than mouse models, canine AD shares important features of the human version. For example, in both humans and dogs AD has been linked to abnormal blooms of Staphyloccocus bacteria on the skin – mostly Staphyloccocus aureus in humans, and Staphyloccocus pseudintermedius in dogs.

In the study, the research team, comprised of veterinary dermatologists, microbiologists, pathologists, and primary scientists, tracked the bacterial populations, or “microbiomes,” on dogs’ skin, and key properties of the skin’s barrier function during an occurrence of AD, and again after standard treatment with antibiotics. During the flare, researchers observed a sharp decrease in the diversity of the skin bacterial population as certain bacterial species proliferated, along with a decrease in the skin’s protective barrier. With antibiotic therapy, both measures returned to normal levels.

“In both canine and human atopic dermatitis we hypothesize there is a similar relationship among skin barrier function, the immune system, and microbes, even if the individual microbe species aren’t identical,” said senior author Elizabeth A. Grice, PhD, an assistant professor of Dermatology and Microbiology at the Perelman School of Medicine at the University of Pennsylvania. “The hope is that insights gained from this study and others like it will enable us one day to treat this condition by altering the skin’s microbiome without antibiotics.”

Thirty-two dogs (15 with canine AD, and 17 without) from Penn Vet’s Ryan Hospital were enrolled in the study. On three occasions – first during AD flares in the affected dogs, then after 4-6 weeks of targeted antibiotics, and finally 4-6 weeks after treatment concluded – the team took swabs from several areas of skin on the affected dogs. They surveyed the microbiomes of these samples by amplifying and sequencing copies of a key bacterial gene whose DNA sequence is distinct for different bacterial species.

Samples from the dogs with ongoing AD had almost ten times the proportion of Staphylococcus species, compared to the control dogs. Corynebacterium species also rose, as they typically do in humans with AD. A standard measure of the diversity of the dogs’ skin microbiomes also decreased sharply, indicating that the abnormal bacterial proliferation – chiefly from S. pseudintermedius – had crowded out other, harmless or potentially beneficial bacterial species.

At the second visit, immediately following completion of antibiotic therapy, the abundance of Staphyloccocus and Corynebacterium on the skin of affected dogs and the diversity of their skin microbiome had returned almost to the levels seen in the control dogs. Those measures remained largely the same in the third visit, after antibiotic therapy was finished.

Impairment in the skin’s ability to work as a “barrier” to keep moisture in and harmful bacteria out is considered a possible factor in triggering or advancing AD. Under the guidance of Elizabeth Mauldin, DVM DACVP, DACVD, an associate professor of Dermatopathology in Penn’s School of Veterinary Medicine, the researchers also tested skin barrier function in the dogs at each of their three visits. Results showed that the low-bacterial-diversity state of AD flares – corresponding to lesions of AD on the skin – correlated with impairments in the skin barrier, as indicated by a standard test of the water loss rate through the skin (TEWL).

“We don’t know if the bacterial overgrowth is weakening the skin’s barrier function or a weakening of the barrier is enabling the bacterial overgrowth, but we do know now that they’re correlated, and that’s a novel finding,” Grice said.

The research team is now conducting further studies of the microbiome in canine atopic dermatitis, in particular to determine how antimicrobial therapy promotes bacterial resistance.

“This investigation is a prime example of the One Health approach to research, a recognition that we’re dealing with the same disease processes in animals and in humans,” said lead author Charles Bradley, VMD, DACVP, a lecturer and dermatopathologist of pathobiology in Penn’s School of Veterinary Medicine. “The findings highlight the importance of dogs as a model for human dermatitis and help lay the groundwork for new therapeutic strategies, for example involving microbiome transplants to compete with the harmful bacterial overgrowth, as an alternative to antibiotic therapy.”

Source:  University of Pennsylvania media release

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