Out today in the European Respiratory Journal: our lab’s newest study looking at the role of the microbiome in critical illness. Our team, led by Rishi Chanderraj, studied the effects of anti-anaerobic antibiotics (which deplete the gut of protective bacteria) on clinical outcomes. In a cohort of >3,000 mechanically ventilated patients, early exposure to anti-anaerobic antibiotics was associated with a 7% absolute increased in 30-day mortality. This effect persisted when controlled for potential confounders, and we recapitulated it in two mouse models (both infectious and non-infectious).

The gut microbiome is an organ. When we devastate it with anti-anaerobic antibiotics, we induce organ failure. This has consequences in our patient’s immunity, metabolism, and susceptibility to infections. We are worried that this common clinical practice is hurting our patients.

Huge congratulations to Rishi and the rest of the team!

Link to manuscript

Link to Twitter walk-through

Link to news release

Rishi Chanderraj

The American Thoracic Society has again agreed to host “A Hands-On Introduction to Studying the Lung Microbiome,” a recurring one-day Post-Graduate Course chaired by Robert Dickson along with Alexa Pragman and Leo Segal.

The course will be held in Washington D.C. on Saturday, May 20, one day before the start of the 2023 American Thoracic Society International Conference.

Topics covered will include:

• An introduction to thinking about the microbiome

• Contaminomics

• Integrating microbiome findings with our disease models

• Longitudinal microbiome studies

• Studying viruses and fungi in lung microbiome studies

• A hands-on introduction to microbiome analysis

• Microbial-host interactions

• Metagenomics and metatranscriptomics

• Analytics for integrative microbiome studies

• Integrative, therapeutic, and environmental applications in microbiome studies

Additional details (speakers, registration information) will follow.

Katie Winner successfully passed her graduate program’s Checkpoint 2, in which she proposed and defended the research that will ultimately form her dissertation. Congrats, Katie!

Katie Winner

Jenn Baker shared her work on this week at the GRC Biology of Acute Respiratory Infection conference in Ventura, California. She shared exciting translational data exploring how depletion of gut anaerobes does (and doesn’t) alter susceptibility to pneumonia. Manuscript out soon!

Robert Dickson and an all-star team of lung microbiome investigators have published a Perspective in the American Journal of Respiratory and Critical Care Medicine on “Therapeutic Targeting of the Respiratory Microbiome.”

“Across the spectrum of acute and chronic respiratory disease, respiratory microbiota are detectable, viable, and variable across patients (2–5); correlated with disease status and severity (1); associated with airway and alveolar inflammation (5, 6); metabolically active and immunologically consequential (7, 8); predictive of clinical outcomes (9–11); influenced by environment and geography (6, 12); and causally involved in disease pathogenesis in animal models (11, 13).

Given these insights, we believe it is prudent to consider the respiratory microbiome as an unexploited, understudied therapeutic target: a biologically potent element of respiratory homeostasis, variable across patients, that may be more readily modifiable than other sources of patient heterogeneity, such as host genomes or comorbidities. In this Perspective, we delineate the anticipated opportunities and challenges related to clinically modulating the respiratory microbiome, which refers to the communities of microbes within the human respiratory tract and their associated ecological milieu.”

Manuscript (American Journal of Respiratory & Critical Care Medicine)

Jezreel Pantaleón García

For several years, Robert Dickson has been working with medical student Jezreel Pantaleón García and his mentor Scott Evans (both at MD Anderson) to study the effects of immune modulation on lung microbiota. Last year, this team published the observation that augmenting lung immune tone (via an inhaled agonist of TLR2, TLR6, and TLR9) has no appreciable effect on the lung bacteria of healthy mice. This study suggests that the known correlation between lung microbiota and lung immunity is more likely due to the host responding to dynamic changes in lung microbiota (rather than vice versa).

As a follow-up to that work, and as a service to all of us who study respiratory microbiota in mice, Jezreel led the way in a newly published letter: “Minimizing caging effects in murine lung microbiome studies.” We know that mice that are cohoused together converge in their respiratory and gut microbiota, which can result in false clustering due to “batch effects” from cohousing. If you house your mice by intervention, you’ll inevitably find differences in their microbiota, but you won’t know if it’s due to your intervention or the fact that cohoused mice cluster together.

To tackle this problem, Jezreel proposes a thoughtful and coherent solution: stratified random cohousing. “In stratified random strategies, originally cohoused mice are randomly distributed for caging with mice from all experimental groups. Then, additional stratified randomization to new cages is performed following each intervention.”

Failure to consider batch effects due to cohousing is a recurring limitation of murine microbiome studies. We hope this simple (and free) strategy will be of use to the field.

Manuscript (Am J Physiol Lung Cell Mol Physiol)

Jenn Baker has been awarded the inaugural Novy Scholarship by the University of Michigan’s Department of Microbiology & Immunology! This new award given to M&I PhD students studying bacteriology, and honors the memory of Frederick George Novy.

Congratulations, Jenn!

Katie Winner has been selected to join the Molecular Mechanisms in Microbial Pathogenesis (MMMP) T32 Training Program. The MMMP Training Grant has a strong tradition of supporting pre-doctoral and post-doctoral trainees with an interest in microbial pathogenesis, and is directed by Professors Vern Carruthers (Director) and Adam Lauring (Associate Director).

Congrats, Katie!

Katie Winner

Jenn Baker

Graduate student Jenn Baker’s abstract was selected for an oral presentation at the 2022 Gordon Research Seminar (September 10-11, Ventura Beach Marriott, California). Congrats, Jenn!

Gordon Research Seminar: Host-Pathogen Interactions During Pulmonary Health and Disease

Gordon Research Conference: Biology of Acute Respiratory Infection

Our team, led by Piyush Ranjan (lab bioinformaticist), has a new publication in Bioinformatics introducing SNIKT, a new software package we developed that automatically visualizes and removes adapter contamination from sequencing data. Adapters are short sequences added to nucleotide sequences to facilitate barcoding and sequencing. They are easily removed if you already know the adapter sequence, but this is often not the case with publicly available datasets. Our tool lets you quickly and effectively remove adapter contamination even if you don’t know the adapter sequence, and is platform-agnostic (works both on Illumina short reads and nanopore-derived long reads).

“SNIKT” stands for Slicing Nucleotides Into Klassifiable Tequences. “SNIKT” is the sound that Wolverine’s claws make when they emerge (we are Wolverines, after all). The “K” and “T” are loving winks to the error rate of nanopore sequencing.

SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data

Manuscript (Bioinformatics)

Download SNIKT (GitHub)

Piyush Ranjan

Robert Dickson and his collaborators Hakam Tiba and Kathleen Stringer have been awarded a grant via the 2022 Massey TBI Grand Challenge. They will use a swine model of traumatic brain injury and experimental microbiome modulation to determine if and how gut bacteria can contribute to and protect from severe traumatic brain injury.

Our group is interested in bringing sequencing technology to the bedside to improve the rapid diagnosis of infections, and have previously demonstrated the potential of real-time metagenomics to identify respiratory pathogens in a clinically relevant timeframe. Among the barriers to this goal is that we can now generate metagenomic data faster than our bioinformatic tools can make sense of it. A problem with many specimens (e.g., respiratory) is the astronomical host:bug ratio. In metagenomic sequencing results from sputum or bronchoalveolar lavage fluid, human DNA overwhelms microbial DNA by a ratio of >99.9:00.1, and you burn all of your time and computational resources classifying human sequences.

For several years, we’ve been working with Jenna Wiens and Meera Krishnamoorthy (Computer Science & Engineering) to address this problem using machine learning. We’re excited to share AMAISE: A Machine Learning Approach to Index-Free Sequence Enrichment. This tool uses machine learning to perform "in silico host depletion," so you can jump faster to microbial classification. It quickly and accurately identifies and excludes host-derived sequences… no need for time-intensive alignment of human sequences.

AMAISE: a machine learning approach to index-free sequence enrichment

Manuscript (Communications Biology)

Download AMAISE (GitHub)

Meera’s blog post about AMAISE

Rishi Chanderraj MD

Lab member Rishi Chanderraj has accepted a faculty position in the Division of Infectious Diseases at the University of Michigan. He will be an Assistant Professor, and in July will start at the Ann Arbor Veterans Affairs Hospital. Rishi will continue to study the role of the gut microbiome in ICU infections and clinical outcomes. Congrats, Rishi!

Robert Dickson will deliver a “State of the Art” lecture at this year’s Aspen Lung Conference. His talk will be on June 8th and will be titled “The Role of Gut and Lung Microbiota in Calibrating Lung Immunity.”

Link to event website

At the American Thoracic Society International Conference, lab members won the following awards:

• Robert Dickson: Mid-Career Peer Recognition Award (Pulmonary Infections and Tuberculosis Assembly)

• Rishi Chanderraj: Abstract Scholarship

• Reid McCallister: Abstract Scholarship

Congrats!

Everyone did a spectacular job sharing their science at ATS. So proud of all of them!

Just published online in the Blue Journal: “Therapeutic Targeting of the Respiratory Microbiome,” a Perspective piece by Robert Dickson and other leaders in the study of the respiratory microbiome.

In the past decade, we’ve learned the the respiratory microbiome is 1) detectable in health, 2) altered in disease, 3) variable across patients, 4) correlated with lung immunity, 5) predictive of disease outcomes, and 6) modified by in-use therapies (e.g. antibiotics and oxygen). All of this makes the respiratory microbiome an attractive potential “treatable trait” for future clinical trials.

But what will it take in order for us to modulate the respiratory microbiome therapeutically? In this essay, we explore what is known and what would need to be known before we can achieve this goal.

Manuscript: Therapeutic Targeting of the Respiratory Microbiome (American Journal of Respiratory and Critical Care Medicine)

We said goodbye to Brooke and Danny, and debated whether beavers know what they’re doing.

Robert Dickson has been appointed Associate Chief for Research for the Division of Pulmonary and Critical Care Medicine at the University of Michigan. He will work closely with MeiLan Han (Division Chief) to advance the Division’s research mission, including team science initiatives, faculty recruitments, and collaborations with other investigators from around the University.

Just published in PLOS ONE: a new study by Kale Bongers and our group teasing out how much of the effects of antibiotics on murine metabolism are due 1) to changes in gut microbiota vs 2) behavioral changes (e.g. food and water aversion due to bad-tasting antibiotics.

A common approach in murine microbiome studies is to put a cocktail of antibiotics (often ampicillin, metronidazole, vancomycin, neomycin) into their drinking water and ascribe all biologic consequences to perturbation of the microbiome. But this overlooks important off-target effects of antibiotics, including food and water avoidance. Metronidazole especially is extremely bitter. Your mice are thus potentially dehydrated and starved at the time of your measurements or experimental exposures.

In this study, we systematically studied the effects of multiple antibiotic regimens (both oral and systemic) on mice: their food and water consumption, their body composition (via NMR), their organ- and tissue-specific metabolism, and their gut bacterial density and community composition.

We found that mice are even more avoidant of water when it contains metronidazole than when it contains a commercial bitterant (denatonium benzoate, the stuff they put antifreeze and animal deterrents and nail-polish). Much of the metabolic consequences previously reported in that common four-drug regimen (ampicillin, metronidazole, vancomycin, neomycin) may actually be due to dehydration and starvation. But we did find that other enteral regimens (cefoperazone, enrofloxacin/ampicillin) can effectively deplete gut bacteria without causing nearly as much food and water avoidance. Interestingly, systemic antibiotics (intraperitoneal ceftriaxone) also result in decreased food and water consumption, suggesting that the microbiome plays a role in behavior (food and water aversion) independent of the direct aversive effects of taste.

The gut microbiome is an important and overlooked player in systemic metabolism, both in health and critical illness. Kale’s study gives us a firm methodological footing for future work determining how the microbiome modulates tissue-specific and organismal metabolism.

Manuscript: Antibiotics cause metabolic changes in mice primarily through microbiome modulation rather than behavioral changes (PLOS ONE)

Kale Bongers MD PhD