TABLE I.

Associations of microbiota with allergic diseases

Article	Topic	Associations with microbiota
Chen et al, Arch Intern Med, 2007	Association of Helicobacter pylori with allergic diseases	H pylori acquisition associates with reduced allergy and asthma risk in children.
Dellon et al, Gastroenterology, 2011		EoE associates with decreased odds of H pylori infection.
Marri et al, J Allergy Clin Immunol, 2013	Association of microbiome with asthma severity	Asthmatic patients had an increase in Proteobacteria. The microbiome of patients with mild asthma is more similar to that of patients with severe asthma than that of healthy control subjects.
Prince et al, Pediatr Clin North Am, 2015	Review article on the species of bacteria and risk of allergy	Children who had allergy had lower loads of Bacteroides, Bifidobacteria, Enterococci, and more Clostridia. Cesarean sections are associated with less microbial diversity and lower Bacteroides, Bifidobacteria, and Escherichia coli and increased Klebsiella, Enterobacter, and Enterococcus species and Clostridia. Similar effects were seen with birth order and antibiotic use. Food allergy data rely largely on animal models. One study with proved egg allergy showed decreased risk with a dog or older siblings in the home. Patients with cow’s milk allergy had more Clostridium and Atopobium species.
Benitez et al, Microbiome, 2015	Study of microbiome in patients with EoE and control subjects	Patients with EoE had increased Proteobacteria, including Neisseria and Corynebacterium species, with increased Granulicatella and Campylobacter species during food-induced active inflammation.
Arrieta et al, Sci Transl Med, 2015	Influence of microbiome on asthma risk	Decrease in Faecalibacterium, Lachnospira, Veillonella, and Rothia species was seen in the gut microbiome of children at 3 mo of age who were at risk for asthma.
Durack et al, J Allergy Clin Immunol, 2016	Atopy, asthma, and inhaled corticosteroid response	Asthmatic patients had an increase in Haemophilus, Neisseria, Fusobacterium, and Porphyromonas species and Sphingomonadaceae and a decrease in Mogibacteriaceae and Lactobacillales
Fujimura et al, Nat Med, 2016	Association and mechanistic evidence that the gut microbiota at 3 mo influences the risk of atopy and asthma	Infants at risk for asthma had a gut microbiome depleted of Bifidobacteria, Lactobacillus, Faecalibacterium, Akkermansia, and Malassezia species (mycobiome) and increased Rhodotorula and Candida species. The predicted metabolome was proinflammatory, and there were decreased numbers of regulatory T cells and ratios of CD4+IFN- γ+/CD4+IL-4+ cells in vitro.
Marrs and Flohr, Pediatr Infect Dis J, 2016	Excellent review of literature on microbiome and food allergy/eczema	Increased gut microbiotic diversity at 3 mo is generally protective for eczema, but specific constituents of the microbiome vary between studies. Increased cutaneous Staphylococcus aureus colonization associates with eczema severity. It is possible that gut diversity promotes greater oral tolerance to foods.
Forsberg et al, Clin Exp Allergy, 2016	Review on the use of prebotics and probiotics for allergy prevention	Meta-analyses conclude that probiotics can prevent eczema but not other allergic disorders.
Zheng et al, PLoS One, 2016	Case-control study of infants with eczema versus control subjects	Patients with eczema were colonized with bacteria known to be associated with atopy (Faecalibacterium prausnitzii and Ruminococcus gnavus) and decreased intestinal barrier (Akkermansia muciniphila). Anti-inflammatory bacteria (Bacteroides fragilis and Streptococcus salivarius) were reduced.
Harris et al, PLoS One, 2016	Microbiome in adult and pediatric patients with EoE compared with GERD and healthy control subjects	Increased but not distinct bacterial load was found in patients with EoE, with predominance of Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria.
Stein et al, N Engl J Med, 2016	Study of Amish versus Hutterite children in relation to endotoxin levels, microbial composition of house dust	Both populations were genetically similar, but Hutterite children had higher serum IgE levels; more asthma; more exposure to cockroach, dust mites, cats, and dogs; and lower levels of endotoxin. Dust from Amish homes was protective for allergen-induced asthma in mice.
Birzele et al, Allergy, 2017	Study of microbiotic diversity in farm-exposed children in relation to nasal sample-derived microbiota	Farm exposure associated with increased bacterial diversity in mattresses and was greater with exposure to straw and cows. Asthma was related to bacterial diversity, although to a lower extent with mucosal samples, suggesting that not just the type of bacteria but also potentially bacterial products are important. Clostridium and Facklamia were abundant in mattresses associated with farming.
Depner et al, J Allergy Clin Immunol, 2017, in press	Association of nasal versus throat microbiota with asthma in rural children	Asthmatic children had decreased bacterial diversity and increased Moraxella species overgrowth that was asthma related only in nonfarm children. The nasal but not the throat microbiome associated with asthma.
Dzidic et al, J Allergy Clin Immunol, 2017, in press	Gut IgA coated-bacteria at 1 and 12 mo in pediatric patients with and without allergy/asthma by 7 y of age	Children with asthma and allergy had lower proportions of IgA-coated bacteria compared with healthy control subjects, and the coated bacteria were different between the 2 groups, with asthmatic patients having higher diversity of IgA-coated Bacteroidetes and Proteobacteria than control subjects.

This table is representative of the literature published close to 2016. A complete comprehensive review is out of the scope of this article, but many excellent reviews on the microbiome and allergy are available.

EoE, Eosinophilic esophagitis; GERD, gastroesophageal reflux disease.