Of possible interest: #PLOSOne paper on #microbiome sharing between children, livestock and household surfaces

Quick post here:

Of possible interest: Microbiome sharing between children, livestock and household surfaces in western Kenya in PLOS One.  Abstract below

The gut microbiome community structure and development are associated with several health outcomes in young children. To determine the household influences of gut microbiome structure, we assessed microbial sharing within households in western Kenya by sequencing 16S rRNA libraries of fecal samples from children and cattle, cloacal swabs from chickens, and swabs of household surfaces. Among the 156 households studied, children within the same household significantly shared their gut microbiome with each other, although we did not find significant sharing of gut microbiome across host species or household surfaces. Higher gut microbiome diversity among children was associated with lower wealth status and involvement in livestock feeding chores. Although more research is necessary to identify further drivers of microbiota development, these results suggest that the household should be considered as a unit. Livestock activities, health and microbiome perturbations among an individual child may have implications for other children in the household.


Quick post: Drosophila Genotype Influences Commensal Bacterial Levels in Lab Reared Flies

Just a quick post here.  This is an interesting paper on how genotype of Drosophila influences their microbiome. As a side story – I think flies could become an interesting and useful model for studying how the built environment (e.g., vials, cages, food, etc) influence microbiomes.

Host genotype can influence the composition of the commensal bacterial community in some organisms. Composition, however, is only one parameter describing a microbial community. Here, we test whether a second parameter—abundance of bacteria—is a heritable trait by quantifying the presence of four commensal bacterial strains within 36 gnotobiotic inbred lines of Drosophila melanogaster. We find that D. melanogaster genotype exerts a significant effect on microbial levels within the fly. When introduced as monocultures into axenic flies, three of the four bacterial strains were reliably detected within the fly. The amounts of these different strains are strongly correlated, suggesting that the host regulates commensal bacteria through general, not bacteria-specific, means. While the correlation does not appear to be driven by simple variation in overall gut dimensions, a genetic association study suggests that variation in commensal bacterial load may largely be attributed to physical aspects of host cell growth and development.

Source: Drosophila Genotype Influences Commensal Bacterial Levels

Paper of interest: Environmental Viral Metagenomics Analyses in Aquaculture

Just a quick post here.  Studies of the microbiology of built environments that house animals (e.g., aquaria, farms, animal shelters, zoos, etc) are of growing interest for multiple reasons.  In that regard this paper might be of interest to some – because it covers some topics that are sometimes neglected in this general area – viral diversity and aquaculture.  Here is a link to the paper

Source: Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Backyard chickens linked to increasing Salmonella outbreaks

Wikipedia Commons (Fir0002/Flagstaffotos)
Wikipedia Commons (Fir0002/Flagstaffotos)

So I feel like this shouldn’t need to be said… but clearly it does.  Don’t kiss chickens or bring them into your bedroom.  Should my opinion not carry enough weight, simply check out this new report from the CDC “Outbreaks of Human Salmonella Infections Associated with Live Poultry, United States, 1990—2014”.  Abstract below.  Major highlights include the fact that almost half the respondents reported keeping poultry indoors and 13% reported kissing chickens.  Not surprisingly there’s been a big increase in poultry-associated Salmonella outbreaks during the last decade or so, the same timeframe where urban chickens have taken off.   I think chickens are great, I have egg-laying chickens at my house… but I don’t kiss them.

Backyard poultry flocks have increased in popularity concurrent with an increase in live poultry—associated salmonellosis (LPAS) outbreaks. Better understanding of practices that contribute to this emerging public health issue is needed. We reviewed outbreak reports to describe the epidemiology of LPAS outbreaks in the United States, examine changes in trends, and inform prevention campaigns. LPAS outbreaks were defined as ≥2 culture-confirmed human Salmonella infections linked to live poultry contact. Outbreak data were obtained through multiple databases and a literature review. During 1990—2014, a total of 53 LPAS outbreaks were documented, involving 2,630 illnesses, 387 hospitalizations, and 5 deaths. Median patient age was 9 years (range <1 to 92 years). Chick and duckling exposure were reported by 85% and 38% of case-patients, respectively. High-risk practices included keeping poultry inside households (46% of case-patients) and kissing birds (13%). Comprehensive One Health strategies are needed to prevent illnesses associated with live poultry.

Dragons and their Microbiomes – really

OK so I love Komodo dragons.  I love microbes and microbiomes.  And I am an editor at mSystems.  So yes I am biased in all sorts of ways about this paper.  So with that caveat – I think this is definitely worth a look: The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat by Embriette R. Hyde, Jose A. Navas-Molina, Se Jin Song, Jordan G. Kueneman, Gail Ackermann, Cesar Cardona, Gregory Humphrey, Don Boyer, Tom Weaver, Joseph R. Mendelson III, Valerie J. McKenzie, Jack A. Gilbert, Rob Knight
mSystems Aug 2016, 1 (4) e00046-16; DOI: 10.1128/mSystems.00046-16.



Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon ( Varanus komodoensis ) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon’s environment are similar to the Komodo dragon’s salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals’ environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

Time to Rethink your Eggs?

New research findings have provided helpful conclusions to help you become a more conscientious consumer of eggs. As summarized in this news article, findings related to animal health, consumer health, worker health, environmental impact, and affordability are outlined. The three housing types they looked at were battery cages, enriched colony housing (arguably more humane than the conventional cages), and cage-free.

Here’s the breakdown and key findings:

image from Flickr under creative commons permission
image from Flickr under creative commons permission


(1) The low levels of shedding and prevalence of Salmonella (a bacteria that can make chickens and consumers sick) was similar between the 3 housing types studied.

(2) The highest microbial quantities were found on the eggs and litter area of the cage-free system, and on the scratch pad in the enriched colony housing. High microbial load isn’t necessarily a bad thing. Given that Salmonella prevalence was similar in all housing types, I don’t think this finding has much weight towards animal, consumer, nor worker health. This point is echoed by the findings that the immune systems of the hens and the effectiveness of their Salmonella vaccinations was not correlated with housing type.

That said, the eggs of the cage-free system and the scratch pads in the enriched colony housing also showed to have the highest levels of total aerobes and coliforms. These are parameters used to measure the sanitary level of food and/or water. Again, this isn’t a direct health and food safety concern in my opinion, especially since it was found that there are just higher microbial loads in these samples already.

(3) The study found that dry belt manure removal systems were helpful in removing Campylobacter species from the chicken’s living space. Dry belt manure removal systems are automatic conveyer belts that catch manure and remove it from the cages typically found in a conventional cage setup. Campylobacter is the most common cause of food poisoning in the US.


The cage-free setup creates a much worse environment for workers compared to the other setups. The findings point to poorer air quality for the workers including, “significantly higher concentrations of airborne particles and endotoxin – toxic components of bacteria”. The article also points out ergonomic concerns for workers repeatedly picking eggs off of the floor.


Egg quality was similar in all 3 housing types, but did correlate with the diet of the hens. The nutrition of the feeds depends not on the housing type, but on the farm itself. The better diets are obviously correlated with more expensive operating costs. The conventional, battery cage setup is the cheapest to operate and for consumers. Eggs from an enriched colony setup would cost an average of 14% more and eggs from a cage-free system would cost an average of 36% more than eggs from a conventional setup.


There is a lot of social pressure today to be conscientious consumers. In terms of consumer health, animal health, worker health, and affordability, this study provides solid evidence that conventional farms are the best way to go.

However, even though there wasn’t evidence for it in this study, I do believe there is a better taste/quality/nutrition associated with non-conventionally farmed eggs. I speak from experience, not science, when I say that. I also think it is important to mention that this study excludes findings related to humane conditions, which is arguably the most important part of the pressure to be an educated consumer. There are two functioning definitions of humane: (1) the animal has at least the bare minimum of what it needs to survive (2) Animals are in an environment where they can move around, express their natural behaviors, and be exposed to natural light and air. Of course animal ‘happiness’ is much harder to quantify, but there are industry standards to measure this that weren’t included in this study.


Diversity of indoor arthropods increases in ‘affluent’ neighborhoods 

There is an interesting new open access paper on urban ecosystems out in Biology Letters: Exoskeletons and economics: indoor arthropod diversity increases in affluent neighbourhoods | Biology Letters

No it is not directly about microbes but nobody’s perfect and many of the arthropods they look at are small and the story about biodiversity is (I think) of interest to those studying microbes in the built environment.

Here is the abstract:

In urban ecosystems, socioeconomics contribute to patterns of biodiversity. The ‘luxury effect’, in which wealthier neighbourhoods are more biologically diverse, has been observed for plants, birds, bats and lizards. Here, we used data from a survey of indoor arthropod diversity (defined throughout as family-level richness) from 50 urban houses and found that house size, surrounding vegetation, as well as mean neighbourhood income best predict the number of kinds of arthropods found indoors. Our finding, that homes in wealthier neighbourhoods host higher indoor arthropod diversity (consisting of primarily non-pest species), shows that the luxury effect can extend to the indoor environment. The effect of mean neighbourhood income on indoor arthropod diversity was particularly strong for individual houses that lacked high surrounding vegetation ground cover, suggesting that neighbourhood dynamics can compensate for local choices of homeowners. Our work suggests that the management of neighbourhoods and cities can have effects on biodiversity that can extend from trees and birds all the way to the arthropod life in bedrooms and basements.

Authors: Misha Leong, Matthew A. Bertone, Keith M. Bayless, Robert R. Dunn, Michelle D. Trautwein

There are a variety of stories out about it including this one: Richer Homes Are Also Richer in Biodiversity

Worth checking out.


Hen housing trade off study results released

Screen Shot 2016-07-20 at 6.50.36 AM

Just a quick post here.  Multiple stories out about the Laying Hen Housing Research Project by the Coalition for Sustainable Egg Supply that maybe of interest.

From: Hen housing trade offs: Food safety, workers and consumers | Food Safety News

As it turns out, the food stores and restaurant chains promising to sell only cage-free eggs by some date in the future and egg producers have been doing their due diligence when it comes to the housing of laying hens. Recently released findings of the Laying Hen Housing Research Project by the Coalition for Sustainable… Continue Reading

The final results of the study are posted here.

Project to study sea turtle microbiomes in captivity and in the wild

Professor Aubrey Tauer of City University of New York, LaGuardia Community College is running an crowdfunding campaign to support research conducted by her non-profit organization to better understand how sea turtle microbiomes vary in captivity and in wild populations. I asked her to write up something for microBEnet about the project. The campaign ends next week, so check it out soon!

Sea Turtle Wexor Tmg


Recently a non-profit I co-founded (www.curaearth.org) started an Indiegogo fundraiser to compare sea turtle microbiomes in the built environment (aquariums, zoos, and sea turtle rehabilitation centers) to wild populations of endangered sea turtles. Sea turtles in the built environment have special challenges- changes in diet, husbandry, and water quality are all proposed mechanisms for possible changes from wild-type microbimes. Additionally, in zoos and aquariums many of these animals are housed in mixed species exhibits. While more and more research is being done to investigate the built environment of animals, and wildlife in particular, information is rather scarce on marine organisms in both captivity and the wild. Cura Earth’s mission focuses on the intersection of animal, human, and environmental health with all of our other projects to date taking place in the field. We decided that fundraising for a two-part study would allow us to perfect our collection and storage methods before collecting samples from wild sea turtles, and also give us samples to compare to wild-type sea turtle microbiome samples.

We propose several favorable outcomes from this study: information that may be valuable to institutions related to diet and husbandry, possible public health information as sea turtles have been known to transmit zoonotic disease to handlers and consumers of sea turtle meat and eggs, and possibilities for future studies such as time series analysis as sea turtles enter, are treated, and are released or die in wildlife rehabilitation centers. A recent publication, published after starting our fundraising campaign, showed some differences in microbiomes for loggerhead sea turtles who stranded, based on their status (dead/necropsied individuals, those just entering rehabilitation, and those who had been in care for longer) but their small sample size makes interpretations difficult1.

At this time we have until July 22nd to fundraise for year two of this study, which will see us collecting hundreds of samples from sea turtles in Nicaragua, El Salvador, and Mexico. We are excited to tackle some of the challenges inherent in this type of field study, where access to freezers and even electricity will be difficult. While our initial study will focus on female nesting sea turtles, if we raise enough money we can start to look at the microbiome changes associated with life stage by sampling hatchlings and juveniles, as well as eggs, which can fail due to disease. We believe this study is urgent in nature, as rapid changes to the environment are ongoing, not just in temperature but salinity, pH, pollution, and changes to the food web. This pilot data should provide the foundation for long-term studies investigating if and how environmental changes may impact sea turtle microbiomes and how that may affect the long-term survival of their species. This is especially important in the endangered eastern pacific hawksbill, which until recently was assumed to be extirpated until nesting sites were discovered relatively recently and conservation programs were developed to monitor this population, which still exists in low numbers (approximately 500 adult females plus an unknown number of males and juveniles) and is vulnerable not just to disease but to egg poaching and fishing practices that drown juveniles and adults.

Urban microbiomes and urban agriculture

About half the human population now lives in urban environments. In 2008, populations of more developed nations were about 74% urban, while about 44% of residents of less developed countries lived in urban areas. It is projected that 70% of the world population will be urban by 2050, with most urban growth occurring in less developed countries. While there are many benefits to urban living but there are also challenges that arise, such as stress, crime, traffic, pollution and sanitation. As people moved from rural to urban populations in more developed countries during the 20th century, the incidence of asthma rose dramatically. At the same time, the incidence of asthma was much lower in rural communities and in less developed countries. These observations suggest that there may be some health benefits from rural living, such as exposure to microbes and allergens. For example, children with the highest levels of exposure to specific allergens and bacteria during their first year are less likely to have allergic sensitization, suggesting that exposure to high levels of certain allergens and bacteria in early life might be beneficial.

Urban agriculture has grown in popularity and has the potential to benefit human health and environmental sustainability. In addition to nutritional benefits arising from the consumption of fresh vegetables or eggs, these backyard gardens may provide some additional benefits of rural life for city dwellers. Keeping a garden or backyard chickens increases the level of backyard use and exposure to microbes associated with soil and plants, as well as chickens. At this point, we know very little about the microbial consequences of urban agriculture but this is an area of growing interest.

An interesting book chapter was recently published on “Urban Microbiomes and Urban Agriculture: What are the connections and why should we care?” Here the author argues that while much of the research on microbial assemblages in the built environment provides compelling examples of the importance of microbes, these studies provide an incomplete picture of microbial distribution and activity in urban systems. In addition to microbial assemblages within buildings, urban microbiomes  also include assemblages associated with exterior environments, such as building surfaces, roads, urban soils, the phyllosphere of plants, animal and human waste, water distribution systems, drainage systems, streams, and other aquatic habitats. These relatively unexplored environments include backyard gardens. By taking a broader view of the urban microbiome, the author promotes a greater understanding of the roles played by microbes in cities and connections within the urban microbiome. Although it is not open access, it is definitely worth a read.

Backyard chicken housing Davis
Backyard chicken housing in Davis, CA