Leading Edge

VoicesBig Questions in Microbiology
Putting a Stop to Persisters

The Chemistry of Symbiosis

V Is for Virosphere

Valerie Mizrahi

Eric W. Schmidt

Edward C. Holmes

University of Cape Town

University of Utah

University of Sydney

The spread of drug-resistant microbes
and spectre of a ‘‘post-antibiotic’’ world
have made the fight against antimicrobialresistance (AMR) one of the most important scientific challenges of our time. The
threat of AMR has raised critical questions that are profoundly influencing theresearch agenda in all spheres of microbiology. For instance, the development of
new intervention strategies against AMR
demands a deeper understanding of
host-pathogen relationships and how
they evolve during the course of transmission, infection, and disease, as well as
insight into the interplay between andamong pathogens and other microbes
within their host and environmental ecosystems. Likewise, paving the way toward
sterilizing therapies that are effective andfast-acting requires that we come to grips
with the microbial factors that mitigate
antibiotic efficacy, which include, but are
not restricted to, persistence and drug
metabolism, permeation, and efflux. In
the case of bacterial persistence, weneed to move from an essentially operational definition of this phenomenon toward mechanistic understanding of thegenesis, physiology, and metabolic stateof persister cells that can survive prolonged exposure to bactericidal antibiotics and of the role, if any, that drugs
might play in this phenomenon. At
this time of spectacular technologicaladvancement and revolutionary change
in our view of the microbial world, I believethat microbiologists are poised to tackle
these questions head on.

Symbiotic bacteria secrete soluble factors, including small molecules, which influence host survival. These represent thelanguage of bacteria as they communicate with each other and with hosts. In
recent years, interest has increased as it
becomes clear that bacterial small molecules influence human health and disease. However, despite some excellent
results, chemical interactions in humanand other animal microbiota can be very
challenging to accurately assess. How
can we robustly move beyond correlation
to causation? How can we more readily
discover the small molecules that profoundly influence biology, including healthand disease? I suggest that a large partof the problem stems from the very
aspect that gives the field its strength,
its interdisciplinary nature. Because researchers have borrowed from microbiology, medicine, organic chemistry,
analytical chemistry, genomics, andothers, there is inconsistency in the language and methods used by different
labs. It is very difficult for a single investigator to deeply understand all of thesefields. One solution is for the field ofchemical symbiosis to come together
and to set its own standards independent of the patchwork of disciplines on
which it relies. Achieving consistency
will push the field beyond misleading results that are well known to specialists
but that bog down broader understanding of the central importance of chemistry in the microbiota.

How large is the virus universe, thevirosphere? What proportion of this vastarray of viruses cause disease in theirhosts? Although these may seem liketimeless questions, they have taken on a
new importance with the advent of bulk
sequencing (metagenomic) surveys of animal and plant populations. Metagenomics also raises new questions about thediversity of genomic structures in viruses,
and the evolutionary processes thatcreate them, and may provide a fresh
perspective on the factors responsible
for the restricted genome sizes that characterize RNA viruses. The vogue for largescale metagenomics surveys has alreadyrevealed that mixed infections may be thenorm, although the key question now
is whether and how these interactions
impact disease ecology and evolution.
Yet metagenomics may be less informative in perhaps the highest stakes topic
in infectious disease evolution—predicting the next pandemic. Given the vastness and darkness of the virosphere,
metagenomic surveys in animal populations will likely tell us little about which
viruses may eventually emerge in humans, and we still need a nuanced understanding of the factors, both ecologicaland genetic, that help or hinder viruses
to successfully invade new hosts. A
more fruitful approach may be regulargenomic surveillance at the frontline ofdisease emergence, such as live animal
markets or other localities that capture
the human-animal interface.

770 Cell 169, May 18, 2017 ª 2017 Published by Elsevier Inc.

Back to the Disease Triangle

High Tide for Marine Microbes

Host and Pathogen Up Close

Sheng-Yang HeNicole Dubilier

Jorge E. GalánMichigan State University and Howard Hughes
Medical InstituteMax Planck Institute for Marine Microbiology

Yale University School of Medicine

One of the most significant challenges ofthe 21st century is to discover innovative
ways of increasing global crop production
to meet the demands for food from thegrowing human population. A major roadblock to global food sufficiency is persistent loss of staple crops to pathogen infections. Greater efforts are urgently
needed to accelerate the buildup of acomprehensive knowledge base that explains how plant diseases occur; howplants defend against microbial pathogens; and how dynamic climate conditions impact plants, microbes, and theirinteractions.
In 1960, RB Stevens, writing in Plant
Pathology: An Advanced Treatise, formulated the famous ‘‘disease triangle’’concept, proposing that plant disease outbreaks require not only a susceptible
plant and a virulent pathogen, but also
conducive environmental conditions. For
practical reasons, however, most contemporary investigations into plant-microbe
interactions at the molecular level devotelittle effort to understanding why climaticconditions, such as humidity and temperature, have a profound effect on pathogen
virulence and host susceptibility. Moreover, these studies often ignore the potentially pervasive effect a plant’s endogenous microbiome may have on basic
plant health and host-pathogen interactions. The classically accepted paradigms
used to approach plant-pathogen interactions must now change. Future studies ofplant-pathogen interactions (and researchfunding) should increasingly consider themulti-dimensional nature of ‘‘disease-environment-microbiome’’ interactions that are
more reflective of what occur in crop fields
and natural ecosystems.

There is no better sign that the golden
age of marine microbiology is here than
the request of this journal to write a shortcomment about them. Marine microbiology was long considered marginalcompared to heavy hitters such as clinicaland pathogenic microbiology. But without
sea microbes, you would not be able toread these lines. Minute algae in the vastness of the world’s oceans produce theoxygen for every second breath you
take. Marine microbes make up a staggering 98% of the ocean’s biomass, process most of our planet’s greenhousegases, and are rich sources of antimicrobials and pharmaceuticals.
Why did it take so long for us to understand how important marine microorganisms are? We weren’t even able to reliably
count and identify them until a few decades ago. Now, thanks to advances inimaging and sequencing methods, combined with instruments that enable us tocollect samples from the ocean’s surface
to the deep-sea, we are discovering anunprecedented diversity of microbial life
with novel metabolic functions.
What lies ahead? Until recently, wefocused largely on interactions between
microorganisms and their abiotic environment, but recent research has demonstrated the fundamental importance ofthe marine microbiome. We are justbeginning to recognize that interactions
between microorganisms, including viruses, and their symbioses with marine
animals and plants, are critical to the ecology and health of all marine ecosystems
and our biosphere.

New technologies always bring the opportunity to tackle new scientific questions. In this sense, this is an excitingtime to study microbial pathogens, given
the myriad of technological developmentsthat are almost tailor-made for the studyof host-pathogen interactions. The timing
could not be more appropriate, as thedwindling pipeline of new antibiotics
coupled to the relentless emergence ofantibiotic resistance make the study of
microbial pathogens more relevant thanever. Host pathogen interactions occur
at all scales, from populations and wholebody to cells, nanomachines, and individual proteins. Recent advances in imaging
technologies are already transforming thestudy of microbial pathogens at all resolution scales. For example, fluorescenceimaging allowing the examination of
host-pathogen interactions at the singlecell level, reveals unique biology thatstudies of cell populations previously
missed. Single-particle cryoelectron microscopy is profoundly transforming
structural biology, while cryoelectron tomography is providing a detailed view ofprotein complexes and molecular machines at an unprecedented resolution.
Finally, whole-body imaging technologies
catch pathogens in action. Although animal models have been invaluable for thestudy of microbial pathogens, controlledhuman infections studies are increasingly
gaining center stage. It is expected that
this type of studies combined with newdevelopments in non-invasive imaging
technologies such as MRI and PET willbring a new dawn in infectious diseaseresearch.

Cell 169, May 18, 2017 771

Harnessing Bacterial Predators

Exploring Microbial Ecosystems

Targeting Bacterial Effectors

Alan Davidson

Gautam Dantas

Chihiro Sasakawa

University of Toronto

Washington University School of Medicine

Chiba University

The recent renaissance in bacteriology
has been fueled largely by our fear of antibiotic-resistant strains as well as by ourgrowing appreciation that our microbial
companions—our microbiome—are essential to our health. While the threat ofantibiotic resistance has challenged us
to develop new approaches for killing
bacteria, we have also learned that broad
spectrum antibiotics, previously thought
to be the ideal treatments, may cause severe collateral damage to our microbiota,
potentially leading to long-term deleterious effects on the immune system, gut
health, and other yet to be discovered
processes. Thus, the big question is:
how can we target anti-bacterial therapies
so that they will kill only the noxious
strains without affecting the health of ourmicrobiome? While this is a challenging
problem, it has already been solved bybacteriophages, nature’s most prevalent
bacterial predators. Phages are highly
specific in their choice of bacterial host,and the receptor proteins that mediate
this specificity are generally identifiable.
Coupling these host-recognition machineries to appropriate bactericidal platforms
is an approach with great promise for thetreatment of bacterial diseases. The ability to specifically target any bacterial
strain will also allow us to address fundamental ‘‘cause and effect’’ questions
relating to the impact of specific species
in the microbiome, something that iscurrently impossible.

In 1683, Antonin van Leeuwenhoek
observed that ‘‘animalcules’’ from hismouth ‘‘were in such enormous numbers,that all the water.seemed to be alive.’’
This appreciation of microbes naturally
living in multi-species ecosystems lostfavor with the clinical focus on singleagent microbial etiologies of pathogenesis, driven by the pioneering work of
Pasteur and Koch in the 1850s. Recentdemocratization of multi-omics technologies has enabled a renaissance in studying culture-unbiased, real-world microbial
ecosystems. In particular, metagenomic
sequencing continues to illuminate theirvast, unexplored taxonomic and functional diversity. A major bottleneck withinterpreting multi-omics data are its analysis, based on principles gleaned from atiny set of axenically cultured microbes.
Remarkably, the functions of nearly a thirdof the E. coli proteome is unannotated,
despite this being the most extensively
studied microbe. Accordingly, microbiology needs truly disruptive technologicalinnovations to reproduce and manipulate
complete, diverse, natural microbial communities in artificial environmental such as
soil mesocosms, and living host habitats,for instance experimental mice. We needto enable high-throughput functional characterization of novel predicted genes andpathways, and computationally predict
novel functions of genes, pathways, andmicrobes with sparse prior knowledge
from remote homologs. This will enableboth derivation of new fundamental basic
science insights from multi-omics microbial community data and translation of these
into novel microbial therapeutic and biotechnological modalities.

According to an old Chinese proverb, ‘‘if
you know the enemy and know yourself,
you need not fear the results of a hundredbattles.’’ This may be a helpful perspective when we pursue new strategies tocombat pathogens or develop new typesof antimicrobial drugs or vaccines. Gut
bacterial pathogens possess sophisticated secretion machinery, including thetype III and type IV secretion systems,by which they deliver a diverse array ofproteins, called effectors, into the gut mucosa. Thus, the pathogens can subvert
host defenses and manipulate cellularsignaling for their own benefit. Our gut
mucosa has multiple layers of defense
against microbial intrusion, but the
mucosal barriers are often compromised
during bacterial infection, allowing bacterial colonization, and in some cases
dissemination into deeper tissues, leading
to severe diseases. These bacterial effectors, as well as their host cellular targets,have attracted a great deal of attention,
because they are essential for bacterial
infection and often share functional similarities in their enzymatic activities. The
discovery of small compounds that canspecifically inhibit them is a promising
approach for creation of new types ofantimicrobial drugs. Recent studies havealso revealed numerous bacterial effectors that interfere with host immune responses during infection, an important
tactic to ensure bacterial survival within
the host. Attacking these effectors could
help improve live vaccines by eliminating
the bacterial arsenal.

772 Cell 169, May 18, 2017