Call for Papers MoBE 2017 Microbiome Special Issue

Call for Papers: MoBE 2017 Special Issue of BioMed Central’s Microbiome Journal  (Submission Guidelines)

We invite submissions of MoBE papers highlighting recent research and emerging hot topics along the theme of “MoBE Research to Applications” for our peer-reviewed MoBE special issue.

Publishing charges are sponsored by the MoBE meeting and BioMed Central’s Microbiome Journal. This special issue will be available by October 1st, 2017.

Please share this announcement among your MoBE colleagues !! 


March 1: paper topic submission (2-3 sentence outline).

These can be submitted via the MoBE 2017 contact form.

June 1:        full paper submission deadline

July 30:      reviews complete, notice to submitters

August 30: revisions due to BioMed Central’s Microbiome Journal

GSC19 (Brisbane, Australia) Registration is Open !!

We are happy to announce that registration for GSC19 is now open !!

Theme:  Extending Standards to Viruses and Microbial Eukaryotes
Date: May 15th-17th, 2017
Location: Stamford Plaza, Brisbane, Australia
Host: Philip Hugenholtz          
Australian Centre for Ecogenomics, University of Queensland
The agenda is packed with exciting sessions and topics:
  • Viral classification and genome standards
  • Microbial eukaryote classification and genome standards
  • Bioinformatic workflow standards (large scale, reproducible, cost-effective)
  • Microbiomes of Australia
  • Modes and tempo of evolution
  • Genome taxonomy
Check out specific session details and confirmed speakers on the GSC19 homepage.  Please direct GSC19 inquiries to the GSC contact page.
Meeting Organizers:Philip Hugenholtz, Caroline Moniz, Lynn Schriml, Folker Meyer and Pelin Yilmaz
We are looking forward to seeing you in Brisbane !!

New papers on Microbiology of the Built Environment, January 29, 2017

Microbes indoors

Building-related symptoms are linked to the in vitro toxicity of indoor dust and airborne microbial propagules in schools: A cross-sectional study – JT Salin – Environmental Research ($41.95)

Graphical abstract

We examined whether the in vitro toxicity of indoor samples from school buildings was associated with work-related health symptoms (building-related symptoms, BRS). Administrators of the Helsinki City Real Estate Department selected 15 schools for the study, and a questionnaire on symptoms connected to work was sent to the teachers in the selected schools for voluntary completion. The cellular toxicity of classroom samples was determined by testing substances extracted from wiped indoor dust and by testing microbial biomass that was cultured on fallout plates. (…) Teachers working in classrooms where the samples showed high sperm toxicity had more BRS. The boar sperm cell motility inhibition assay appears promising as a tool for demonstrating the presence of indoor substances associated with BRS.

Microbial rRNA sequencing analysis of evaporative cooler indoor environments located in the Great Basin Desert region of the United States – Angela R. Lemons – Environmental Science: Processes & Impacts (£42.50)

Graphical abstract

(…) The objective of this study was to determine if the increased humidity previously reported in EC homes leads to varying microbial populations compared to homes with air conditioners (AC). Children with physician-diagnosed allergic rhinitis living in EC or AC environments were recruited into the study. Air samples were collected from the child’s bedroom for genomic DNA extraction and metagenomic analysis of bacteria and fungi using the Illumina MiSeq sequencing platform. The analysis of bacterial populations revealed no major differences between EC and AC sampling environments. The fungal populations observed in EC homes differed from AC homes. The most prevalent species discovered in AC environments belonged to the genera Cryptococcus (20%) and Aspergillus (20%). In contrast, the most common fungi identified in EC homes belonged to the order Pleosporales and included Alternaria alternata (32%) and Phoma spp. (22%). The variations in fungal populations provide preliminary evidence of the microbial burden children may be exposed to within EC environments in this region.

Molecular approaches for the detection and monitoring of microbial communities in bioaerosols: A review – Keunje Yoo – Journal of Environmental Sciences

Graphical abstract

Bioaerosols significantly affect atmospheric processes while they undergo long-range vertical and horizontal transport and influence atmospheric chemistry and physics and climate change. Accumulating evidence suggests that exposure to bioaerosols may cause adverse health effects, including severe disease. Studies of bioaerosols have primarily focused on their chemical composition and largely neglected their biological composition and the negative effects of biological composition on ecosystems and human health. Here, current molecular methods for the identification, quantification, and distribution of bioaerosol agents are reviewed. Modern developments in environmental microbiology technology would be favorable in elucidation of microbial temporal and spatial distribution in the atmosphere at high resolution. In addition, these provide additional supports for growing evidence that microbial diversity or composition in the bioaerosol is an indispensable environmental aspect linking with public health.

Reflections on the history of indoor air science, focusing on the last 50 years – Jan Sundell – Indoor Air ($6 to rent, $38 to own).

From the preview

The scientific articles and Indoor Air conference publications of the indoor air sciences (IAS) during the last 50 years are summarized.(…) The modern scientific history started in the 1970s with a question: “did indoor air pose a threat to health as did outdoor air?” Soon it was recognized that indoor air is more important, from a health point of view, than outdoor air. Topics of concern were first radon, environmental tobacco smoke and lung cancer, followed by volatile organic compounds, formaldehyde and sick building syndrome, house dust mites, asthma and allergies, Legionnaires disease and other airborne infections. Later emerged dampness/mold-associated allergies and today’s concern with “modern exposures-modern diseases.” Ventilation, thermal comfort, indoor air chemistry, semi volatile organic compounds, building simulation by computational fluid dynamics, and fine particulate matter are common topics today. From their beginning in Denmark and Sweden, then in the USA, the indoor air sciences now show increasing activity in East and Southeast Asia.

Forensic microbes

The background story was even more chillingFrozen: Thawing and Its Effect on the Postmortem Microbiome in Two Pediatric Cases – Jennifer L. Pechal – Forensic Sciences ($6 to rent, $38 to own).

Taxonomic hierarchies of the 16S rRNA gene amplicon analysis performed with QIIME throughout the thawing process.

Previous postmortem microbiome studies have focused on characterizing taxa turnover during an undisturbed decomposition process. How coexisting conditions (e.g., frozen, buried, burned) affect the human microbiome at the time of discovery is less well understood. Microbiome data were collected from two pediatric cases at the Wayne County Medical Examiner in Michigan. The bodies were found frozen, hidden in a freezer for an extended time. Microbial communities were sampled from six external anatomic locations at three time points during the thawing process, prior to autopsy. The 16S rRNA V4 gene amplicon region was sequenced using high-throughput sequencing (Illumina MiSeq). Microbial diversity increased, and there was a distinct shift in microbial community structure and abundance throughout the thawing process. Overall, these data demonstrate that the postmortem human microbiome changes during the thawing process, and have important forensic implications when bodies have been substantially altered, modified, and concealed after death.

Microbes on a plane

Assessment of the Bacterial Diversity of Aircraft Water: Identification of the Frequent Fliers – Harald Handschuh  – PLOS ONE (OA)

Number of isolates within each bacterial class identified across the aft and fwd galley of a fleet of short haul aircraft.

The aim of this study was to determine and identify bacteria inhabiting the supply chain of an airline’s drinking water using phenotypic and 16S rDNA sequence-based analysis. Water samples (n = 184) were sourced from long-haul and short-haul aircraft, the airline water source and a water service vehicle. In total, 308 isolates were characterised and their identity determined, which produced 82 identified bacterial species belonging to eight classes: γ-Proteobacteria; β-Proteobacteria; α-Proteobacteria; Bacilli; Actinobacteria; Flavobacteria; Sphingobacteria and Cytophaga. Statistical differences in bacterial diversity were found to exist across sampling locations (X2 = 39.220, p = 0.009) and furthermore, differences were observed (X2 = 15.475, p = 0.030) across aircraft type (long- or short-haul). This study demonstrates the diverse nature of microorganisms within the aircraft drinking water supply chain. To the best of our knowledge, this is the most extensive study undertaken to date of microbial diversity in aircraft drinking water.

Microbes and food production

Differential Attachment of Salmonella enterica and Enterohemorrhagic Escherichia coli to Alfalfa, Fenugreek, Lettuce, and Tomato Seeds – Applied and Environmental Microbiology – Yue Cui ($25 for one day)

Fenugreek seeds. Source: Wikipedia.

Vegetable seeds have the potential to disseminate and transmit foodborne bacterial pathogens. This study was undertaken to assess the abilities of selected Salmonella and enterohemorrhagic Escherichia coli (EHEC) strains to attach to fungicide-treated vs. untreated, and intact vs. mechanically-damaged seeds of alfalfa, fenugreek, lettuce, and tomato. Surface-sanitized seeds (2 g) were exposed to 4 individual strains of Salmonella or EHEC at 20°C for 5 h. (…) Unit weight of lettuce seeds had the highest numbers of attached Salmonella or EHEC cells, followed by tomato, alfalfa, and fenugreek seeds. In contrast, individual fenugreek seeds had more attached pathogen cells followed by lettuce, alfalfa, and tomato seeds. Significantly more Salmonella and EHEC cells attached to mechanically-damaged seeds than to intact seeds (P < 0.05). Although on average, significantly more Salmonella and EHEC cells were recovered from untreated, than fungicide-treated seeds (P < 0.05), fungicide treatment did not significantly affect the attachment of individual bacterial strains to vegetable seeds (P > 0.05), with a few exceptions. This study fills gaps in the current body of literature and helps explain bacterial interactions with vegetable seeds with varying surface characteristics.

Microbiological Load of Edible Insects Found in Belgium – Rudy Caparros Megido – Insects (OA)

Toffee coconut mealworms, from:

(…) this study aims to characterize the microbial load of edible insects found in Belgium (i.e., fresh mealworms and house crickets from European farms and smoked termites and caterpillars from a traditional Congolese market) and to evaluate the efficiency of different processing methods (blanching for all species and freeze-drying and sterilization for European species) in reducing microorganism counts. All untreated insect samples had a total aerobic count higher than the limit for fresh minced meat (6.7 log cfu/g). Nevertheless, a species-dependent blanching step has led to a reduction of the total aerobic count under this limit, except for one caterpillar species. Freeze-drying and sterilization treatments on European species were also effective in reducing the total aerobic count. Yeast and mold counts for untreated insects were above the Good Manufacturing Practice limits for raw meat, but all treatments attained a reduction of these microorganisms under this limit. These results confirmed that fresh insects, but also smoked insects from non-European trades, need a cooking step (at least composed of a first blanching step) before consumption. Therefore, blanching timing for each studied insect species is proposed and discussed.

Human Microbiome Congress San Diego

This is not directly related to the topic of this blog, but possibly of interest for some readers here. A couple of days ago, I attended the Human Microbiome Congress in San Diego, and I live-tweeted all the talks that I attended. The result is a collection of over 400 tweets, which I brought together in this Storify of the Human Microbiome Congress San Diego.

Future Proofing Law symposium at #UCDavis #futureproofinglaw #AI #algorithms #robots #CRISPR

This may be of interest to some here.  I made a Storify of the Tweets from the “Future Proofing Law” symposium that was at UC Davis yesterday and the day before.  There were multiple biotech. themed sessions and presentations as well as discussions of many topics connected to microBEnet in various ways such as open scholarship, synthetic biology, intellectual property, machine learning, and more.

Humans as collectors and emitters of environmental microbes

As part of the Healthy Buildings 2015 America Conference, there was a technical session on Indoor Microbiome Research where we discussed strategies on, among other things, how to sample and analyze bioaerosols using modern high throughput sequencing techniques. In that workshop, we did a small exercise highlighting the potential for humans to transport microbes into different settings. Prior to the session, one of the panelists (names protected) left the room and handled a fruiting body of a puffball known as Pisolithus tinctorius. Attendees of the workshop were invited to swab those of us on the panel and our possessions in explore if we could later identify which panelist handled the specimen. We used this is a springboard to talk about potential issues in microbiome sampling – spatial variation in microbial communities, do we need duplicate samples, how much pressure to apply and what size area to swab?

Pisolithus tinctorius, also known as the dog turn fungus.

The fungal sequences from those dozen swabs from that workshop were pretty clear: the dog turd fungus appeared on swabs from the targeted panelist’s hands, computer, and chair. In fact, it was second most abundant fungus in those samples and not present at all from swabs of other panelists.

I think about these results in the context of different routes of microbial transmission. Occupants and their activities are a large determinant of the bioaerosols in indoor spaces, and there are thought to be three routes of “occupant emissions”:

  1. Direct shedding from the human envelope (shedding, spitting, etc)
  2. Resuspension of microbes that have settled in the indoor environment (“reservoir” microbes)
  3. A transport vector of microbes collected in other spaces, as in our session

It’s always been a concern in occupational settings for workers not to bring harmful substances on their clothing to the home setting, where in this case it would be workers transporting microbes into their home and creating an opportunity for direct transmission or subsequent resuspension from surfaces in the home.

For a more comprehensive understanding of indoor bioaerosols, it’s important to know the strengths of these three different transmission routes. Teasing apart the relative contributions of these three processes which sum to create a Snoopy-inspired Pig-Pen model of aerosol generation can be challenging.

Some research is tackling this challenge by using environmental chambers. For example, (bio)aerosol particle emissions were approximately 6 times greater when occupants walked around a chamber, compared to when they were sitting. While some of the increased particles were associated increased vigor of upper body movements, most was attributable to release of particles from the floor. In another study, the air in a small chamber with an occupant sitting and wearing minimal clothing can show a unique microbial signature as to identify the individual occupant, showing that direct shedding is detectable when other sources are sufficiently removed. Recently, a study focusing on particles shed from the human envelopment and aiming to minimize resuspsension from the floor linked aerosol release from different activities with personal exposure. For questions about cross-contamination in indoor environments, these kinds of studies can help us better understand the nature of occupant emissions.

Wrap up of #PSB17 – Pacific Symposium in Biocomputing

Just got back from the Pacific Symposium in Biocomputing. The meeting had some aspects that may be of interest to various folks.

Electronic proceedings of the meeting are here.

I talked in a session on functional predictions.  I was asked to do this at the last minute so I made my slides by hand. Here they are.


I also recorded audio of my talk. Have not synched it to the slides but this may be of interest to some.


And I made a Storify of Tweets related to the meeting:


Summary and talks/slides from Workshop on the Microbiome of the International Space Station

Public Domain Image

Just a quick post here that all the information (including slides and videos) from a really interesting CASIS sponsored workshop are online.  The topic relates to the most extreme built environment to date… the International Space Station.   The workshop was called “Exploring the Microbiome/Immunome and Disease on the International Space Station” and took place back in October.  Both Jonathan and I were invited but were unable to go… it’s a shame because it sounded really cool.

Is “Immunome” really a word though?


Meeting Report: Microbiomes of the Built Environment #3 – Day 2

Report on Day 2 of the “Microbiomes of the Built Environment: From Research to Application”.  My report and Storify of tweets from Day 1 can be found here.

Session #1 “Beyond Bacteria: Viral and Fungal Ecology in Indoor Environments”

First speaker was Linsey Marr “Viruses in the Built Environment”.  Talking about their work looking at seasonality of viruses in daycare centers, detailed studies of Influenza A, and others.  Interesting finding that viruses were more concentrated outdoors than indoors, and that similar numbers of bacteria and viruses were found.  Described a vertical concentration gradient of particles, but only a 15% difference in exposure between 1 meter and 2 meters from floor. Described how airborne viruses are subject to aerosol dynamics.

Next was John Taylor “Fungi in the Built Environment”.  Started off talking about the Rachel Adams study in student housing at Berkeley where they found that dispersal and geography/season were the primary drivers of fungal populations (not occupant behavior).  Found the reverse for bacteria (affected by occupants).  Showing data that shedding is less important than resuspension of environmental microbes.  Several studies showing that indoor air looks a lot like outdoor air, with some extra bacteria from people.  Talked about practical implications of this work, for example with litigation around poorly maintained buildings.

Session #2 “Built Environment Interventions and the Microbiome: Impacts and Tradeoffs”

Mark Mendell went next with “Changing Indoor Microbial Environments to Benefit Human Health: What Do We Know?”. Started off by saying how much more complicated we have made our knowledge about microbes in the built environment.  Basically reviewed the entire literature on health effects.  He talked about which microbial/environmental factors are correlated with positive or negative health outcomes.  Too hard to summarize here!  See the Storify below for more details, I’m going to try to get his slides to post here.

Then Michael Waring “Bio-walls and Indoor Houseplants: Facts and Fictions”.  He talked about the various claims being made in the world about the cleansing effects of plants.  He then went back to the famous NASA study (that we’ve blogged about in the past) and went through the literature and basically concluded that to have any effect at all you would need more plants per square meter than could possibly fit in the space.  At a high air exchange rate you would need 500 potted plants per square meter!  Then he talked about bio-walls, which he showed could theoretically actually clean air.  However, there are a number of disadvantages of biowalls in terms of emitting other VOCs, humidity concerns, and cost.  His conclusion was that for air cleaning, we’d be better off with just increased ventilation.

Session #3 “Perspectives from Building Design and Commissioning”

Started with Kevin van den Wymelenberg “What the Design Community Needs to Incorporate Consideration of the Microbiomes of the Built Environment Into the Design of Facilities”.  Kevin is an architect and he presented that perspective to the audience.  Talked about the possible tradeoff between energy and health and the need to harness the creativity of architects.  In a similar vein he talked about the need to excite people about our results and the importance of engaging architects, engineers, and industry.

Last talk (remote) of the meeting was Robin Guenther.  My computer died *and* her talk title wasn’t in the program so I don’t know the title.  But basically she posed 4 key questions, from a healthcare architect perspective, that she thinks should be answered.  She made the point that architects make choices that influence health, but don’t always think of it that way.   She discussed the move to “tight” buildings and wondered what effect that will have on the microbiome.  Informed us that hospitals are driving much of the product development in antimicrobial materials.

Meeting Report: Microbiomes of the Built Environment – Meeting #3: Day 1

Today was the first day of the 3rd meeting in the NAS-sponsored series of “Microbiomes of the Built Environment:  From Research to Application” meetings.  This meeting was held at UC Irvine and the goal was to provide information for the NAS committee that will subsequently produce a report on the status of the field.  For anyone that missed the talks, everything was recorded and will be available online.   We’ll post here at microBEnet when that happens.  The Storify of Twitter is at the end of this post.

Session #1 “How the Built Environment Microbiome Responds to Context and Perturbations”

The first speaker was Janet Jansson “Microbial Community Response to Environmental Conditions and the ‘Microbiomes in Transition (MinT)’ Initiative”.  She described a changing world (climate change, disease, chemical/drug exposure) where the impact on microbial communities is largely unknown.  Talked about a “multi-omics” approach for studying complex and changing environments.   Gave a few examples including permafrost and mice.

Next was Sarah Evans who talked about “Soil Microbial Responses to Climate Perturbations”.  Showed examples in soil, where manipulation of drought conditions causes a major shift in the microbiome.  Microbial communities show a change in ecological strategy, via taxonomic shifts.  Most of these shifts are caused by the arrival of new taxa to the system. Talked about rain microbial communities which I hadn’t though much about, however doesn’t see a large signature of those things in soils.

Last in the intro session was Shelly Miller “The Effect of Geographic Location on the Composition and Function of Indoor Microbiomes”.  Talked about their 1200 US homes study, their detailed Boulder dorm study, and the Boulder flood study.  Summarized part of their results with “If you want to change the fungi you live with, move somewhere else, preferably far away.  If you want to change the bacteria, change who you live with”.  Showing data that only a few fungi were more present inside homes than outside, more for bacteria but still only a few % of the total.  Broad scale metadata (climate, geography) predict fungal composition but not bacterial composition.  The dorm study showed that they could predict the sex of occupants from the bacterial communities.   The flood study showed that flood homes have different bacterial/fungal communities even after remediation.

Individual talks

Rob Knight gave a special talk called “The Current Toolkit for Studying Microbiome/Built Environment Interfaces”.  Talked about the big data aspect of microbiology and the dramatic changes in the field over the last 15 years.  Started with a lot of discovery data, early microbiome studies, etc.  Talked about the need for more accurate taxonomic assignments (examples of subway anthrax study, and the high abundance of platypus samples in Finland).  Hard to summarize his talk, he summarized the entire field!  Some data I hadn’t seen before about the spatial distribution of metabolic products and their relationship to bugs.

Another special talk about Scott Jackson “Microbiome and Metagenomic Standards at NIST”.  Gave some background on NIST.   Talked about various standards they’ve developed, including a human DNA standard for clinical diagnostics and an RNA spike-in standard for microarrary experiments.  They even have a highly characterized antibody molecule as a standard.  Describing the transition to a world where microbes themselves are therapeutics (as opposed to proteins or isolated molecules).  Talked about the fact that microbiome studies have so many places for error, from collection to extraction to analysis.  They are potentially interested in developing a mock community standard, but make the point that existing ones aren’t used.

Session #2 “Expanding the Toolkit: Studying Microbial Functions”

First talk was by Jay Lennon “A trait-based approach to microbial diversity”.  Pointing out the limitation of studying lists of taxa.  Asking about the phylogenetic conservation of traits, trade-offs between traits, and different kinds of traits.  Talked about bacterial persistence and longevity.  Claimed that 90% of skin bacteria were either dead or dormant.

Other talk in this session was from Pieter Dorrestein “Chemistry of the human habitat…”.  Started off describing the significant lack of knowledge regarding indoor chemistry.  Need that groundwork before we can relate that to microbes and the whole system. Talked mostly about what I would call chemical forensics, matching chemical signatures on between people and the objects that surround them.

Session #3 “Expanding the Toolkit: Modeling the Microbiome”

First up was Jennifer Martiny “Microbial biogeography in light of traits”  As with Jay Lennon’s talk, an emphasis on traits versus lists of taxa.  Mentioned the Doolittle argument that because of HGT and rapid evolution, taxonomy might not be as informative as we hope.  However, she went on to show data that in fact there is a strong phylogenetic signal among microbes.  Gave some neat examples about microbial traits.

Next in session was Patricia Fabian (remotely) “Modeling the Built Environment, Indoor Air Quality, and Health: A Systems Science Approach”.  Talked about the challenges facing models, including multi-factorial nature, rare diseases, insufficient power in most studies, etc.  But, did show the advantages of the modeling approach… giving some interesting examples including influenza survival and impact of weatherization on low income multi family housing.

Session #4 “Analyzing What’s Known from Case Examples: Comparing and Contrasting Results”

Tiina Reponen “Microbiomes of the Built Environment: Homes”.  She started of by listing those attributes that make homes different from hospitals and the ISS (this is a comparative session).  Those were pets, influence of outdoor fungi, humidity, and building materials.  Showed the effects of various home characteristics on microbial richness, abundance, spores, etc.  Then made the point that what we really want to know is the relationship to health effects.  Talked in depth about the CCAAPS study, where they looked at homes over a long time. Also discussed the ERMI index (Environmental Relative Moldiness Index) which is a PCR-based assay that appears to be predictive in infants of later development of asthma.

Next was Brandon “Bubba” Brooks, “Reviewing major themes in hospital microbiome research”.  Gave a good background on hospital work.  Talked about the NICU as both and important and tractable study system.  Showed source-tracking data about where microbes on touch surfaces in the hospital come from.  Emphasized the need for genome sequencing, strain-level differences are important.  Summarized differences between hospitals and houses.  Hospitals are more sourced from humans, more spatial separation, etc.

Last talk in this group was Kasthuri Venkateswaran “Venkat” talking about “Environmental “omics on the ISS”.  Talking about Planetary Protection and why NASA cares about the microbiome.  NASA has access to some really cool closed systems, not just the ISS but various testing facilities including underwater.  Gave some geography of the ISS.  Talked about the results of a large-scale survey of the ISS, did both culture-dependent and culture-independent methods.  Looked at both bacteria and fungi.

Afterwards we had breakout sessions for discussing the status of the field and then a poster session.  Here is the Storify of tweet for the day: