Biology & Life Sciences

Pearls: The Microbiome

Published September 1, 2021 Curated Collections

Human-associated microbial communities can include eukaryotes, archaea, bacteria and viruses and provide protection against foreign invaders, stimulate the immune response, produce antimicrobials, and aid in digestion among other functions. Our understanding of the link between the human microbiome and disease is rapidly expanding.

In this collection, PLOS Pathogens presents a range of Pearls articles delving into the current state of knowledge linking the microbiome to human disease.

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USCDCP, Public Domain

PLOS Pathogens Editorial overview of Pearls Microbiome Series: E pluribus unum
August 31, 2021 Deborah A. Hogan, Joseph Heitman, Mary Ann Jabra-Rizk, Laura J. Knoll, John M. Leong, Neal Silverman

The human microbiome constitutes the collection of all the microorganisms living in association with the human body...
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10.1371/journal.ppat.1009690 CC BY 4.0

PLOS Pathogens Helminth-mediated disease tolerance in TB: A role for microbiota?
July 15, 2021 Danielle Karo-Atar, Nargis Khan, Maziar Divangahi, Irah L. King

Intestinal helminth infections are most prevalent in peri-equatorial regions of the world and have an overlapping geographical distribution…
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10.1371/journal.ppat.1008208 CC BY 4.0

PLOS Pathogens B vitamin acquisition by gut commensal bacteria
January 23, 2020 Emily E. Putnam, Andrew L. Goodman

The mammalian gut microbiome is one of the densest known microbial communities. These microbial communities are…
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10.1371/journal.ppat.1008684 CC BY 4.0

PLOS Pathogens Decades-old studies of fungi associated with mammalian lungs and modern DNA sequencing approaches help define the nature of the lung mycobiome
July 30, 2020 Paris S. Hamm, John W. Taylor, Joseph A. Cook, Donald O. Natvig

The vertebrate lung is the organ with the largest surface area presented to the external environment. The combined alveolar surface area…
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10.1371/journal.ppat.1008558 CC BY 4.0

PLOS Pathogens How MHCII signaling promotes benign host-microbiota interactions
June 29, 2020 Mary Melissa Roland, Ahmed Dawood Mohammed, Jason Lee Kubinak

The major histocompatibility complex (MHC) is a hyper-polymorphic gene-dense region found on Chromosome 6 in humans…
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10.1371/journal.ppat.1008540 CC BY 4.0

PLOS Pathogens Salmonella finds a way: Metabolic versatility of Salmonella enterica serovar Typhimurium in diverse host environments
June 11, 2020 Savannah J. Taylor, Sebastian E. Winter

Infection with nontyphoidal Salmonella strains, such as Salmonella enterica serovar Typhimurium (S. Typhimurium) commonly…
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10.1371/journal.ppat.1008524 CC BY 4.0

PLOS Pathogens Microbiome factors in HPV-driven carcinogenesis and cancers
June 4, 2020 Daniel Lin, Ramez Kouzy, Joseph Abi Jaoude, Sonal S. Noticewala, Andrea Y. Delgado Medrano, Ann H. Klopp, Cullen M. Taniguchi, Lauren E. Colbert

Human papillomavirus (HPV) infections account for over 600,000 new cancer cases every year. HPV is implicated in approximately…
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10.1371/journal.ppat.1008398 CC BY 4.0

PLOS Pathogens Drosophila as a model for the gut microbiome
April 23, 2020 William B. Ludington, William W. Ja

The microbiome has tremendous potential to impact host physiology and metabolism. Gut bacteria in particular have been linked to…
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10.1371/journal.ppat.1008370 CC BY 4.0

PLOS Pathogens In sickness and health: Effects of gut microbial metabolites on human physiology
April 9, 2020 Robert W. P. Glowacki, Eric C. Martens

The connection between intestinal microbes and human health has been appreciated since the 1880s with Theodor Escherich’s investigation of Escherichia…
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10.1371/journal.ppat.1008353 CC BY 4.0

PLOS Pathogens The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions
April 2, 2020 Jessica R. Galloway-Peña, Dimitrios P. Kontoyiannis

Extensive efforts have focused on investigating the contributions of the intestinal microbiome to health and disease, including immunomodulation…
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10.1371/journal.pntd.0003044 CC BY 4.0

PLOS Pathogens 5 challenges in understanding the role of the virome in health and disease
March 26, 2020 David Wang

Over the past decade, many studies have established linkages between the microbiome and states of health and disease. By contrast…
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10.1371/journal.ppat.1008234 CC BY 4.0

PLOS Pathogens Virus interactions with bacteria: Partners in the infectious dance
February 11, 2020 Ursula Neu, Bernardo A. Mainou

The outcome of viral infection depends on the interplay between host factors and the environment. Host factors, like the expression…
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10.1371/journal.ppat.1008212 CC BY 4.0

PLOS Pathogens Gastrointestinal organoid technology advances studies of enteric virus biology
January 30, 2020 Abimbola O. Kolawole, Christiane E. Wobus

The historical lack of models recapitulating the complexity of the human intestinal epithelium has hindered studies into many aspects of human enteric virus…
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CDC CC0

PLOS Pathogens Novel and emerging sources of Clostridioides difficile infection
December 19, 2019 Nicholas A. Turner, Becky A. Smith, Sarah S. Lewis

Clostridioides difficile causes more healthcare-associated infections in the United States than any other pathogen, with an estimated 500,000 infections…
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10.1371/journal.ppat.1007912 CC BY 4.0

PLOS Pathogens Parasite-microbe-host interactions and cancer risk
August 15, 2019 Nolwenn M. Dheilly, Paul W. Ewald, Paul J. Brindley, Raina N. Fichorova, Frédéric Thomas

Characterizing the factors that disrupt the cellular barriers to cancer (e.g., cell-cycle arrest, apoptosis, repression of telomerase, cell adhesion…
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10.1371/journal.ppat.1007861 CC BY 4.0

PLOS Pathogens Helicobacter pylori and colorectal cancer—A bacterium going abroad?
August 8, 2019 Julia Butt, Meira Epplein

Helicobacter pylori is a bacterium that infects the mucus gel layer above the gastric epithelium in approximately half of the world’s population…
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10.1371/journal.ppat.1007727 CC BY 4.0

PLOS Pathogens Microbiome evolution during host aging
July 25, 2019 Francisco Daniel Davila Aleman, Dario Riccardo Valenzano

Commensal microbes and their multicellular eukaryotic hosts constitute a highly integrated system—termed the holobiont…
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10.1371/journal.ppat.1007740 CC BY 4.0

PLOS Pathogens Microbiota-mediated disease resistance in plants
June 13, 2019 Nathan Vannier, Matthew Agler, Stéphane Hacquard

Plant pathogens represent a constant and major threat to global food production, with 20%–30% global crop losses estimated, principally in…
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10.1371/journal.ppat.1007750 CC BY 4.0

PLOS Pathogens Vitamin A at the interface of host–commensal–pathogen interactions
June 6, 2019 Namrata Iyer, Shipra Vaishnava

The gut is a stable ecosystem governed by interactions between the host immune system and trillions of gut-resident microbes…
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10.1371/journal.ppat.1007645 CC BY 4.0

PLOS Pathogens The ABCs of wheeze: Asthma and bacterial communities
April 25, 2019 Naomi G. Wilson, Ariel Hernandez-Leyva, Andrew L. Kau

Asthma is a common respiratory illness affecting approximately 8% of Americans and is characterized by symptoms of wheeze, cough…
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10.1371/journal.ppat.1007586 CC BY 4.0

PLOS Pathogens Covert pathogenesis: Transient exposures to microbes as triggers of disease
March 28, 2019 Nicole M. Gilbert, Amanda L. Lewis

Our understanding of microbial pathogenesis is founded largely on the assumption that the microbe responsible for causing a disease is the…
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10.1371/journal.ppat.1007581 CC BY 4.0

PLOS Pathogens Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract
March 7, 2019 Matthew H. Foley, Sarah O’Flaherty, Rodolphe Barrangou, Casey M. Theriot

Research on bile acids has increased dramatically due to recent studies demonstrating their ability to significantly impact the host, microbiome…
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10.1371/journal.ppat.1007563 CC BY 4.0

PLOS Pathogens The founder hypothesis: A basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens
February 21, 2019 Yael Litvak, Andreas J. Bäumler

Our skin and mucosal surfaces are colonized by diverse microbial communities, collectively known as the microbiota…
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10.1371/journal.ppat.1007479 CC BY 4.0

PLOS Pathogens To B₁₂ or not to B₁₂: Five questions on the role of cobalamin in host-microbial interactions
January 3, 2019 Carol A. Rowley, Melissa M. Kendall

Vitamins are organic compounds that are essential to the health of an organism. Humans cannot synthesize vitamins but obtain vitamins…
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10.1371/journal.pone.0184928 CC BY 4.0

PLOS Pathogens Barrett’s esophagus and esophageal cancer: Links to microbes and the microbiome
December 20, 2018 Teminioluwa A. Ajayi, Sarah Cantrell, Ashley Spann, Katherine S. Garman

Esophageal cancer represents a major problem globally, with an estimated 398,000 esophageal squamous cell cancers…
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10.1371/journal.ppat.1007342 CC BY 4.0

PLOS Pathogens Candida–streptococcal interactions in biofilm-associated oral diseases
December 13, 2018 Hyun Koo, David R. Andes, Damian J. Krysan

The oral cavity contains up to 700 different species of microorganisms, including both bacteria and fungi…
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10.1371/journal.ppat.1007310 CC BY 4.0

PLOS Pathogens Bacteriophages shift the focus of the mammalian microbiota
October 25, 2018 Breck A. Duerkop

For over three centuries, there has been rising interest in and fascination with the complex consortium of microbes that associate…
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10.1371/journal.ppat.1007215 CC BY 4.0

PLOS Pathogens There was collusion: Microbes in inflammatory bowel disease
September 20, 2018 Serre-Yu Wong, Ken Cadwell

Inflammatory bowel disease (IBD) refers to a group of chronic inflammatory diseases that affect the gastrointestinal tract and includes ulcerative…
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10.1371/journal.ppat.1007183 CC BY 4.0

PLOS Pathogens Norovirus interactions with the commensal microbiota
September 6, 2018 Meagan E. Sullender, Megan T. Baldridge

Human norovirus (HNoV) is the leading cause of epidemic nonbacterial gastroenteritis worldwide, causing an acute diarrheal infection…
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10.1371/journal.ppat.1006719 CC BY 4.0

PLOS Pathogens The oral microbiome: A Lesson in coexistence
January 25, 2018 Ahmed S. Sultan, Eric F. Kong, Alexandra M. Rizk, Mary Ann Jabra-Rizk

Whether in human, animal, or microbial communities, the resolve to coexist is the quintessence of survival. Therefore, in natural habitats…
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10.1371/journal.ppat.1004436 CC BY 4.0

PLoS Pathogens The Skin Microbiome: A Focus on Pathogens and Their Association with Skin Disease
November 13, 2014 Keisha Findley, Elizabeth A. Grice

Microbes are present in every environmental niche and live in close association with humans and each other. Members of these communities…
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10.1371/journal.ppat.1008028 CC BY 4.0

PLOS Pathogens Parasite microbiome project: Grand challenges
October 10, 2019 Nolwenn M. Dheilly, Joaquín Martínez Martínez, Karyna Rosario, Paul J. Brindley, Raina N. Fichorova, Jonathan Z. Kaye, Kevin D. Kohl, Laura J. Knoll, Julius Lukeš, Susan L. Perkins, Robert Poulin, Lynn Schriml, Luke R. Thompson

The first Parasite Microbiome Project (PMP) Workshop (January 9–14, 2019, Clearwater, Florida, United States) hosted researchers from…
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10.1371/journal.ppat.1005039 CC BY 4.0

PLOS Pathogens Are Human Intestinal Eukaryotes Beneficial or Commensals?
August 13, 2015 Julius Lukeš, Christen Rune Stensvold, Kateřina Jirků-Pomajbíková, Laura Wegener Parfrey

Since the advent of microbiology, it has been well known that each human body hosts a multitude of microbes. The magnitude…
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10.1371/journal.ppat.1008950 CC BY 4.0

PLOS Pathogens Entamoeba histolytica: Five facts about modeling a complex human disease in rodents
November 12, 2020 Carolina Mendoza Cavazos, Laura J. Knoll

Entamoeba histolytica is an extracellular enteric eukaryotic parasite. Globally, an average of 50 million cases and 55,000 to 100,000 deaths …
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10.1371/journal.ppat.1009056 CC BY 4.0

PLOS Pathogens Strain diversity in the microbiome: Lessons from Bacteroides fragilis
December 10, 2020 Hannah C. Carrow, Lakshmi E. Batachari, Hiutung Chu

The evolutionary history between humans and their microbiota shapes a symbiotic relationship that is integral for host health. Culture-based…

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