No retraction, correction or concern found when last checked on Oct 17, 2026.

Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies

Nikhil Aggarwal, Shohei Kitano, Ginette Ru Ying Puah and 3 more

Chemical Reviews · 2022 · Review

doi:10.1021/acs.chemrev.2c00431

Abstract

The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.

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Byrd A. L.; Belkaid Y.; Segre J. A. The Human Skin Microbiome. Nat. Rev. Microbiol. 2018, 16, 143–155..
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Costello E. K.; Lauber C. L.; Hamady M.; Fierer N.; Gordon J. I.; Knight R. Bacterial Community Variation in Human Body Habitats across Space and Time. Science 2009, 326, 1694–1697..
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Grice E. A.; Kong H. H.; Conlan S.; Deming C. B.; Davis J.; Young A. C.; Bouffard G. G.; Blakesley R. W.; Murray P. R.; et al. Topographical and Temporal Diversity of the Human Skin Microbiome. Science 2009, 324, 1190–1192..
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114.
Grice E. A.; Segre J. A. The Skin Microbiome. Nat. Rev. Microbiol. 2011, 9, 244–253..
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115.
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Scharschmidt T. C.; Fischbach M. A. What Lives on Our Skin: Ecology, Genomics and Therapeutic Opportunities of the Skin Microbiome. Drug Discovery Today Dis. Mech. 2013, 10, e83–e89..
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127.
Shifts in human skin and nares microbiota of healthy children and adults · 2012
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128.
Jo J. H.; Deming C.; Kennedy E. A.; Conlan S.; Polley E. C.; Ng W. I.; Segre J. A.; Kong H. H. Diverse Human Skin Fungal Communities in Children Converge in Adulthood. J. Invest. Dermatol. 2016, 136, 2356–2363..
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Jo J. H.; Kennedy E. A.; Kong H. H. Topographical and Physiological Differences of the Skin Mycobiome in Health and Disease. Virulence 2017, 8, 324–333..
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Kyriakis K. P.; Terzoudi S.; Palamaras I.; Pagana G.; Michailides C.; Emmanuelides S. Pityriasis Versicolor Prevalence by Age and Gender. Mycoses 2006, 49, 517–518..
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Havlickova B.; Czaika V. A.; Friedrich M. Epidemiological Trends in Skin Mycoses Worldwide. Mycoses 2008, 51, 2–15..
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Seebacher C.; Bouchara J. P.; Mignon B. Updates on the Epidemiology of Dermatophyte Infections. Mycopathologia 2008, 166, 335–352..
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134.
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136.
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137.
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Leyden J. J.; Marples R. R.; Kligman A. M. Staphylococcus Aureus in the Lesions of Atopic Dermatitis. Br. J. Dermatol. 1974, 90, 525–530..
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Not in our library10.1186/2045-7022-4-33
140.
Drago L.; De Grandi R.; Altomare G.; Pigatto P.; Rossi O.; Toscano M. Skin Microbiota of First Cousins Affected by Psoriasis and Atopic Dermatitis. Clin. Mol. Allergy 2016, 14, 2.
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141.
Gonzalez M. E.; Schaffer J. V.; Orlow S. J.; Gao Z.; Li H.; Alekseyenko A. V.; Blaser M. J. Cutaneous Microbiome Effects of Fluticasone Propionate Cream and Adjunctive Bleach Baths in Childhood Atopic Dermatitis. J. Am. Acad. Dermatol. 2016, 75, 481–493..
Not in our library10.1016/j.jaad.2016.04.066
142.
Zasloff M. Antimicrobial Peptides, Innate Immunity, and the Normally Sterile Urinary Tract. J. Am. Soc. Nephrol. 2007, 18, 2810–2816..
Not in our library10.1681/asn.2007050611
143.
Wolfe A. J.; Brubaker L. “Sterile Urine” and the Presence of Bacteria. Eur. Urol. 2015, 68, 173–174..
Not in our library10.1016/j.eururo.2015.02.041
144.
The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence · 2014
Not checked
145.
Mansour B.; Monyok A.; Makra N.; Gajdacs M.; Vadnay I.; Ligeti B.; Juhasz J.; Szabo D.; Ostorhazi E. Bladder Cancer-Related Microbiota: Examining Differences in Urine and Tissue Samples. Sci. Rep. 2020, 10, 11042.
Not in our library10.1038/s41598-020-67443-2
146.
Modena B. D.; Milam R.; Harrison F.; Cheeseman J. A.; Abecassis M. M.; Friedewald J. J.; Kirk A. D.; Salomon D. R. Changes in Urinary Microbiome Populations Correlate in Kidney Transplants with Interstitial Fibrosis and Tubular Atrophy Documented in Early Surveillance Biopsies. Am. J. Transplant. 2017, 17, 712–723..
Not in our library10.1111/ajt.14038
147.
Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury · 2012
No notice
148.
Ruiz-Gomez M. L.; Martin-Way D. A.; Perez-Ramirez M. D.; Gutierrez-Fernandez J. Male Deep Infections by Gardnerella Vaginalis. A Literature Review and a Case Report. Rev. Esp. Quimioter. 2019, 32, 469–472.
Not in our library
149.
The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment · 2017
No notice
150.
Bajic P.; Van Kuiken M. E.; Burge B. K.; Kirshenbaum E. J.; Joyce C. J.; Wolfe A. J.; Branch J. D.; Bresler L.; Farooq A. V. Male Bladder Microbiome Relates to Lower Urinary Tract Symptoms. Eur. Urol. Focus 2020, 6, 376–382..
Not in our library10.1016/j.euf.2018.08.001
151.
Groah S. L.; Perez-Losada M.; Caldovic L.; Ljungberg I. H.; Sprague B. M.; Castro-Nallar E.; Chandel N. J.; Hsieh M. H.; Pohl H. G. Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People with and without Bladder Dysfunction. J. Urol. 2016, 196, 579–587..
Not in our library10.1016/j.juro.2016.01.088
152.
Thomas-White K. J.; Gao X.; Lin H.; Fok C. S.; Ghanayem K.; Mueller E. R.; Dong Q.; Brubaker L.; Wolfe A. J. Urinary Microbes and Postoperative Urinary Tract Infection Risk in Urogynecologic Surgical Patients. Int. Urogynecol. J. 2018, 29, 1797–1805..
Not in our library10.1007/s00192-018-3767-3
153.
Komesu Y. M.; Dinwiddie D. L.; Richter H. E.; Lukacz E. S.; Sung V. W.; Siddiqui N. Y.; Zyczynski H. M.; Ridgeway B.; Rogers R. G.; Arya L. A.; et al. Defining the Relationship between Vaginal and Urinary Microbiomes. Am. J. Obstet. Gynecol. 2020, 222, 154.E1–154.E10..
Not in our library10.1016/j.ajog.2019.08.011
154.
Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infectionResearch in context · 2019
Not checked
155.
Johnson G.; Wolfe A. J.; Putonti C. Characterization of the φCTX-Like Pseudomonas Aeruginosa Phage Dobby Isolated from the Kidney Stone Microbiota. Access Microbiol. 2019, 1, e000002.
Not in our library10.1099/acmi.0.000002
156.
Malki K.; Sible E.; Cooper A.; Garretto A.; Bruder K.; Watkins S. C.; Putonti C. Seven Bacteriophages Isolated from the Female Urinary Microbiota. Genome Announce. 2016, 4, e01003-16.
Not in our library10.1128/genomea.01003-16
157.
Khasriya R.; Sathiananthamoorthy S.; Ismail S.; Kelsey M.; Wilson M.; Rohn J. L.; Malone-Lee J. Spectrum of Bacterial Colonization Associated with Urothelial Cells from Patients with Chronic Lower Urinary Tract Symptoms. J. Clin. Microbiol. 2013, 51, 2054–2062..
Not in our library10.1128/jcm.03314-12
158.
Paalanne N.; Husso A.; Salo J.; Pievilainen O.; Tejesvi M. V.; Koivusaari P.; Pirttila A. M.; Pokka T.; Mattila S.; Jyrkas J.; et al. Intestinal Microbiome as a Risk Factor for Urinary Tract Infections in Children. Eur. J. Clin. Microbiol. Infect. Dis. 2018, 37, 1881–1891..
Not in our library10.1007/s10096-018-3322-7
159.
Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection · 2019
No notice
160.
Garretto A.; Miller-Ensminger T.; Ene A.; Merchant Z.; Shah A.; Gerodias A.; Biancofiori A.; Canchola S.; Canchola S.; Castillo E.; et al. Genomic Survey of E. Coli from the Bladders of Women with and without Lower Urinary Tract Symptoms. Front. Microbiol. 2020, 11, 2094.
Not in our library10.3389/fmicb.2020.02094
161.
Lavigne J. P.; Nicolas-Chanoine M. H.; Bourg G.; Moreau J.; Sotto A. Virulent Synergistic Effect between Enterococcus Faecalis and Escherichia Coli Assayed by Using the Caenorhabditis Elegans Model. PLoS One 2008, 3, e3370.
Not in our library10.1371/journal.pone.0003370
162.
Croxall G.; Weston V.; Joseph S.; Manning G.; Cheetham P.; McNally A. Increased Human Pathogenic Potential of Escherichia Coli from Polymicrobial Urinary Tract Infections in Comparison to Isolates from Monomicrobial Culture Samples. J. Med. Microbiol. 2011, 60, 102–109..
Not in our library10.1099/jmm.0.020602-0
163.
Stapleton A. E.; Au-Yeung M.; Hooton T. M.; Fredricks D. N.; Roberts P. L.; Czaja C. A.; Yarova-Yarovaya Y.; Fiedler T.; Cox M.; Stamm W. E. Randomized, Placebo-Controlled Phase 2 Trial of a Lactobacillus Crispatus Probiotic Given Intravaginally for Prevention of Recurrent Urinary Tract Infection. Clin. Infect. Dis. 2011, 52, 1212–1217..
Not in our library10.1093/cid/cir183
164.
Sumati A. H.; Saritha N. K. Association of Urinary Tract Infection in Women with Bacterial Vaginosis. J. Glob. Infect. Dis. 2009, 1, 151–152..
Not in our library10.4103/0974-777x.56254
165.
Gilbert N. M.; O’Brien V. P.; Lewis A. L. Transient Microbiota Exposures Activate Dormant Escherichia Coli Infection in the Bladder and Drive Severe Outcomes of Recurrent Disease. PLoS Pathog. 2017, 13, e1006238.
Not in our library10.1371/journal.ppat.1006238
166.
Ravel J.; Gajer P.; Abdo Z.; Schneider G. M.; Koenig S. S.; McCulle S. L.; Karlebach S.; Gorle R.; Russell J.; Tacket C. O.; et al. Vaginal Microbiome of Reproductive-Age Women. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 4680–4687..
Not in our library10.1073/pnas.1002611107
167.
Antonio M. A.; Hawes S. E.; Hillier S. L. The Identification of Vaginal Lactobacillus Species and the Demographic and Microbiologic Characteristics of Women Colonized by These Species. J. Infect. Dis. 1999, 180, 1950–1956..
Not in our library10.1086/315109
168.
Zhou X.; Bent S. J.; Schneider M. G.; Davis C. C.; Islam M. R.; Forney L. J. Characterization of Vaginal Microbial Communities in Adult Healthy Women Using Cultivation-Independent Methods. Microbiology 2004, 150, 2565–2573..
Not in our library10.1099/mic.0.26905-0
169.
Boskey E. R.; Telsch K. M.; Whaley K. J.; Moench T. R.; Cone R. A. Acid Production by Vaginal Flora in Vitro Is Consistent with the Rate and Extent of Vaginal Acidification. Infect. Immun. 1999, 67, 5170–5175..
Not in our library10.1128/iai.67.10.5170-5175.1999
170.
Vaginal pH and Microbicidal Lactic Acid When Lactobacilli Dominate the Microbiota · 2013
No notice
171.
Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis · 2015
No notice
172.
Distinct Immune Responses Elicited From Cervicovaginal Epithelial Cells by Lactic Acid and Short Chain Fatty Acids Associated With Optimal and Non-optimal Vaginal Microbiota · 2020
No notice
173.
Zhou X.; Brown C. J.; Abdo Z.; Davis C. C.; Hansmann M. A.; Joyce P.; Foster J. A.; Forney L. J. Differences in the Composition of Vaginal Microbial Communities Found in Healthy Caucasian and Black Women. ISME J. 2007, 1, 121–133..
Not in our library10.1038/ismej.2007.12
174.
Zhou X.; Hansmann M. A.; Davis C. C.; Suzuki H.; Brown C. J.; Schutte U.; Pierson J. D.; Forney L. J. The Vaginal Bacterial Communities of Japanese Women Resemble Those of Women in Other Racial Groups. FEMS Immunol. Med. Microbiol. 2010, 58, 169–181..
Not in our library10.1111/j.1574-695x.2009.00618.x
175.
Verstraelen H.; Verhelst R.; Claeys G.; Temmerman M.; Vaneechoutte M. Culture-Independent Analysis of Vaginal Microflora: The Unrecognized Association of Atopobium Vaginae with Bacterial Vaginosis. Am. J. Obstet. Gynecol. 2004, 191, 1130–1132..
Not in our library10.1016/j.ajog.2004.04.013
176.
Peebles K.; Velloza J.; Balkus J. E.; McClelland R. S.; Barnabas R. V. High Global Burden and Costs of Bacterial Vaginosis: A Systematic Review and Meta-Analysis. Sex Transm. Dis. 2019, 46, 304–311..
Not in our library10.1097/olq.0000000000000972
177.
Allsworth J. E.; Peipert J. F. Prevalence of Bacterial Vaginosis: 2001–2004 National Health and Nutrition Examination Survey Data. Obstet. Gynecol. 2007, 109, 114–120..
Not in our library10.1097/01.aog.0000247627.84791.91
178.
Brotman R. M.; Klebanoff M. A.; Nansel T. R.; Yu K. F.; Andrews W. W.; Zhang J.; Schwebke J. R. Bacterial Vaginosis Assessed by Gram Stain and Diminished Colonization Resistance to Incident Gonococcal, Chlamydial, and Trichomonal Genital Infection. J. Infect. Dis. 2010, 202, 1907–1915..
Not in our library10.1086/657320
179.
Brotman R. M.; Bradford L. L.; Conrad M.; Gajer P.; Ault K.; Peralta L.; Forney L. J.; Carlton J. M.; Abdo Z.; Ravel J. Association between Trichomonas Vaginalis and Vaginal Bacterial Community Composition among Reproductive-Age Women. Sex Transm. Dis. 2012, 39, 807–812..
Not in our library10.1097/olq.0b013e3182631c79
180.
Martin H. L.; Richardson B. A.; Nyange P. M.; Lavreys L.; Hillier S. L.; Chohan B.; Mandaliya K.; Ndinya-Achola J. O.; Bwayo J.; Kreiss J. Vaginal Lactobacilli, Microbial Flora, and Risk of Human Immunodeficiency Virus Type 1 and Sexually Transmitted Disease Acquisition. J. Infect. Dis. 1999, 180, 1863–1868..
Not in our library10.1086/315127
181.
Gosmann C.; Anahtar M. N.; Handley S. A.; Farcasanu M.; Abu-Ali G.; Bowman B. A.; Padavattan N.; Desai C.; Droit L.; Moodley A.; et al. Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased Hiv Acquisition in Young South African Women. Immunity 2017, 46, 29–37..
Not in our library10.1016/j.immuni.2016.12.013
182.
Feehily C.; Crosby D.; Walsh C. J.; Lawton E. M.; Higgins S.; McAuliffe F. M.; Cotter P. D. Shotgun Sequencing of the Vaginal Microbiome Reveals Both a Species and Functional Potential Signature of Preterm Birth. npj Biofilms Microbiomes 2020, 6, 50.
Not in our library10.1038/s41522-020-00162-8
183.
Establishment of vaginal microbiota composition in early pregnancy and its association with subsequent preterm prelabor rupture of the fetal membranes · 2019
No notice
184.
Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery · 2019
No notice
185.
Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin · 2018
No notice
186.
Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth · 2018
No notice
187.
The Evolving Facets of Bacterial Vaginosis: Implications for HIV Transmission · 2019
No notice
188.
Han L.; Taub R.; Jensen J. T. Cervical Mucus and Contraception: What We Know and What We Don’t. Contraception 2017, 96, 310–321..
Not in our library10.1016/j.contraception.2017.07.168
189.
The Cervicovaginal Mucus Barrier · 2020
No notice
190.
Domino S. E.; Hurd E. A.; Thomsson K. A.; Karnak D. M.; Holmen Larsson J. M.; Thomsson E.; Backstrom M.; Hansson G. C. Cervical Mucins Carry Alpha(1,2)Fucosylated Glycans That Partly Protect from Experimental Vaginal Candidiasis. Glycoconj. J. 2009, 26, 1125–1134..
Not in our library10.1007/s10719-009-9234-0
191.
Cone R. A. Barrier Properties of Mucus. Adv. Drug. Delivery Rev. 2009, 61, 75–85..
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192.
Agarwal K.; Lewis A. L. Vaginal Sialoglycan Foraging by Gardnerella Vaginalis: Mucus Barriers as a Meal for Unwelcome Guests?. Glycobiology 2021, 31, 667–680..
Not in our library10.1093/glycob/cwab024
193.
Mutual Preservation: A Review of Interactions Between Cervicovaginal Mucus and Microbiota · 2021
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194.
Gipson I. K.; Moccia R.; Spurr-Michaud S.; Argueso P.; Gargiulo A. R.; Hill J. A. 3rd; Offner G. D.; Keutmann H. T. The Amount of Muc5b Mucin in Cervical Mucus Peaks at Midcycle. J. Clin. Endocrinol. Metab. 2001, 86, 594–600..
Not in our library10.1210/jc.86.2.594
195.
Mirmonsef P.; Hotton A. L.; Gilbert D.; Gioia C. J.; Maric D.; Hope T. J.; Landay A. L.; Spear G. T. Glycogen Levels in Undiluted Genital Fluid and Their Relationship to Vaginal Ph, Estrogen, and Progesterone. PLoS One 2016, 11, e0153553.
Not in our library10.1371/journal.pone.0153553
196.
Farage M.; Maibach H. Lifetime Changes in the Vulva and Vagina. Arch. Gynecol Obstet. 2006, 273, 195–202..
Not in our library10.1007/s00404-005-0079-x
197.
Seidman J. D.; Cho K. R.; Ronnett B. M.; Kurman R. J. Surface Epithelial Tumors of the Ovary. In Blaustein’s Pathology of the Female Genital Tract; Springer: 2011; pp 679–784.
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Tester R.; Al-Ghazzewi F. H. Intrinsic and Extrinsic Carbohydrates in the Vagina: A Short Review on Vaginal Glycogen. Int. J. Biol. Macromol. 2018, 112, 203–206..
Not in our library10.1016/j.ijbiomac.2018.01.166
199.
Free Glycogen in Vaginal Fluids Is Associated with Lactobacillus Colonization and Low Vaginal pH · 2014
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200.
Muhleisen A. L.; Herbst-Kralovetz M. M. Menopause and the Vaginal Microbiome. Maturitas 2016, 91, 42–50..
Not in our library10.1016/j.maturitas.2016.05.015
201.
McClelland R. S.; Lingappa J. R.; Srinivasan S.; Kinuthia J.; John-Stewart G. C.; Jaoko W.; Richardson B. A.; Yuhas K.; Fiedler T. L.; Mandaliya K. N.; et al. Evaluation of the Association between the Concentrations of Key Vaginal Bacteria and the Increased Risk of Hiv Acquisition in African Women from Five Cohorts: A Nested Case-Control Study. Lancet Infect. Dis. 2018, 18, 554–564..
Not in our library10.1016/s1473-3099(18)30058-6
202.
Association of the Vaginal Microbiota with Human Papillomavirus Infection in a Korean Twin Cohort · 2013
No notice
203.
Norenhag J.; Du J.; Olovsson M.; Verstraelen H.; Engstrand L.; Brusselaers N. The Vaginal Microbiota, Human Papillomavirus and Cervical Dysplasia: A Systematic Review and Network Meta-Analysis. BJOG 2020, 127, 171–180..
Not in our library10.1111/1471-0528.15854
204.
Lev-Sagie A.; Goldman-Wohl D.; Cohen Y.; Dori-Bachash M.; Leshem A.; Mor U.; Strahilevitz J.; Moses A. E.; Shapiro H.; Yagel S.; et al. Vaginal Microbiome Transplantation in Women with Intractable Bacterial Vaginosis. Nat. Med. 2019, 25, 1500–1504..
Not in our library10.1038/s41591-019-0600-6
205.
Gilbert J. A.; Quinn R. A.; Debelius J.; Xu Z. Z.; Morton J.; Garg N.; Jansson J. K.; Dorrestein P. C.; Knight R. Microbiome-Wide Association Studies Link Dynamic Microbial Consortia to Disease. Nature 2016, 535, 94–103..
Not in our library10.1038/nature18850
206.
Health and disease markers correlate with gut microbiome composition across thousands of people · 2020
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207.
Falony G.; Joossens M.; Vieira-Silva S.; Wang J.; Darzi Y.; Faust K.; Kurilshikov A.; Bonder M. J.; Valles-Colomer M.; Vandeputte D.; et al. Population-Level Analysis of Gut Microbiome Variation. Science 2016, 352, 560–564..
Not in our library10.1126/science.aad3503
208.
Schnorr S. L.; Candela M.; Rampelli S.; Centanni M.; Consolandi C.; Basaglia G.; Turroni S.; Biagi E.; Peano C.; Severgnini M.; et al. Gut Microbiome of the Hadza Hunter-Gatherers. Nature Commun. 2014, 5, 3654.
Not in our library10.1038/ncomms4654
209.
Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population · 2017
No notice
210.
Verdam F. J.; Fuentes S.; de Jonge C.; Zoetendal E. G.; Erbil R.; Greve J. W.; Buurman W. A.; de Vos W. M.; Rensen S. S. Human Intestinal Microbiota Composition Is Associated with Local and Systemic Inflammation in Obesity. Obesity 2013, 21, E607–E615..
Not in our library10.1002/oby.20466
211.
Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing · 2015
No notice
212.
Crovesy L.; Masterson D.; Rosado E. L. Profile of the Gut Microbiota of Adults with Obesity: A Systematic Review. Eur. J. Clin. Nutr. 2020, 74, 1251–1262..
Not in our library10.1038/s41430-020-0607-6
213.
Manichanh C.; Rigottier-Gois L.; Bonnaud E.; Gloux K.; Pelletier E.; Frangeul L.; Nalin R.; Jarrin C.; Chardon P.; Marteau P.; et al. Reduced Diversity of Faecal Microbiota in Crohn’s Disease Revealed by a Metagenomic Approach. Gut 2006, 55, 205.
Not in our library10.1136/gut.2005.073817
214.
Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis · 2019
No notice
215.
Current Understanding of Gut Microbiota in Mood Disorders: An Update of Human Studies · 2019
No notice
216.
Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome · 2016
No notice
217.
Golfetto L.; de Senna F. D.; Hermes J.; Beserra B. T.; França F. d. S.; Martinello F. Lower Bifidobacteria Counts in Adult Patients with Celiac Disease on a Gluten-Free Diet. Arq. Gastroenterol. 2014, 51, 139–143..
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218.
Kerckhoffs A. P.; Samsom M.; van der Rest M. E.; de Vogel J.; Knol J.; Ben-Amor K.; Akkermans L. M. Lower Bifidobacteria Counts in Both Duodenal Mucosa-Associated and Fecal Microbiota in Irritable Bowel Syndrome Patients. World J. Gastroenterol. 2009, 15, 2887–2892..
Not in our library10.3748/wjg.15.2887
219.
Suppression of gut dysbiosis by Bifidobacterium longum alleviates cognitive decline in 5XFAD transgenic and aged mice · 2019
No notice
220.
Kong H. H.; Oh J.; Deming C.; Conlan S.; Grice E. A.; Beatson M. A.; Nomicos E.; Polley E. C.; Komarow H. D.; et al. Temporal Shifts in the Skin Microbiome Associated with Disease Flares and Treatment in Children with Atopic Dermatitis. Genome Res. 2012, 22, 850–859..
Not in our library10.1101/gr.131029.111
221.
Impaired diversity of the lung microbiome predicts progression of idiopathic pulmonary fibrosis · 2018
Not checked
222.
Thomas-White K. J.; Gao X.; Lin H.; Fok C. S.; Ghanayem K.; Mueller E. R.; Dong Q.; Brubaker L.; Wolfe A. J. Urinary Microbes and Postoperative Urinary Tract Infection Risk in Urogynecologic Surgical Patients. Int.Urogynecol. J. 2018, 29, 1797–1805..
Not in our library10.1007/s00192-018-3767-3
223.
Curtiss N.; Balachandran A.; Krska L.; Peppiatt-Wildman C.; Wildman S.; Duckett J. A Case Controlled Study Examining the Bladder Microbiome in Women with Overactive Bladder (Oab) and Healthy Controls. Eur. J. Obstet. Gynecol. Reprod. Biol. 2017, 214, 31–35..
Not in our library10.1016/j.ejogrb.2017.04.040
224.
Joung H.; Chu J.; Kim B.-K.; Choi I.-S.; Kim W.; Park T.-S. Probiotics Ameliorate Chronic Low-Grade Inflammation and Fat Accumulation with Gut Microbiota Composition Change in Diet-Induced Obese Mice Models. Appl. Microbiol. Biotechnol. 2021, 105, 1203–1213..
Not in our library10.1007/s00253-020-11060-6
225.
Cheng Y.-C.; Liu J.-R. Effect of Lactobacillus Rhamnosus Gg on Energy Metabolism, Leptin Resistance, and Gut Microbiota in Mice with Diet-Induced Obesity. Nutrients 2020, 12, 2557.
Not in our library10.3390/nu12092557
226.
Borgeraas H.; Johnson L. K.; Skattebu J.; Hertel J. K.; Hjelmesæth J. Effects of Probiotics on Body Weight, Body Mass Index, Fat Mass and Fat Percentage in Subjects with Overweight or Obesity: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Obes. Rev. 2018, 19, 219–232..
Not in our library10.1111/obr.12626
227.
Larsen N.; Vogensen F. K.; Gøbel R. J.; Michaelsen K. F.; Forssten S. D.; Lahtinen S. J.; Jakobsen M. Effect of Lactobacillus Salivarius Ls-33 on Fecal Microbiota in Obese Adolescents. Clin. Nutr. 2013, 32, 935–940..
Not in our library10.1016/j.clnu.2013.02.007
228.
Gøbel R. J.; Larsen N.; Jakobsen M.; Mølgaard C.; Michaelsen K. F. Probiotics to Adolescents with Obesity: Effects on Inflammation and Metabolic Syndrome. J. Pediatr. Gastroenterol. Nutr. 2012, 55, 673–678..
Not in our library10.1097/mpg.0b013e318263066c
229.
Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila · 2017
No notice
230.
Depommier C.; Everard A.; Druart C.; Plovier H.; Van Hul M.; Vieira-Silva S.; Falony G.; Raes J.; Maiter D.; Delzenne N. M.; et al. Supplementation with Akkermansia Muciniphila in Overweight and Obese Human Volunteers: A Proof-of-Concept Exploratory Study. Nat. Med. 2019, 25, 1096–1103..
Not in our library10.1038/s41591-019-0495-2
231.
Plovier H.; Everard A.; Druart C.; Depommier C.; Van Hul M.; Geurts L.; Chilloux J.; Ottman N.; Duparc T.; Lichtenstein L.; et al. A Purified Membrane Protein from Akkermansia Muciniphila or the Pasteurized Bacterium Improves Metabolism in Obese and Diabetic Mice. Nat. Med. 2017, 23, 107–113..
Not in our library10.1038/nm.4236
232.
Wang Y.; Guo Y.; Chen H.; Wei H.; Wan C. Potential of Lactobacillus Plantarum Zdy2013 and Bifidobacterium Bifidum Wbin03 in Relieving Colitis by Gut Microbiota, Immune, and Anti-Oxidative Stress. Can. J. Microbiol. 2018, 64, 327–337..
Not in our library10.1139/cjm-2017-0716
233.
Jang Y. J.; Kim W.-K.; Han D. H.; Lee K.; Ko G. Lactobacillus Fermentum Species Ameliorate Dextran Sulfate Sodium-Induced Colitis by Regulating the Immune Response and Altering Gut Microbiota. Gut Microbes 2019, 10, 696–711..
Not in our library10.1080/19490976.2019.1589281
234.
A randomised, double-blind, placebo-controlled trial of a multi-strain probiotic in patients with asymptomatic ulcerative colitis and Crohn’s disease · 2019
No notice
235.
Tamaki H.; Nakase H.; Inoue S.; Kawanami C.; Itani T.; Ohana M.; Kusaka T.; Uose S.; Hisatsune H.; Tojo M.; et al. Efficacy of Probiotic Treatment with Bifidobacterium Longum 536 for Induction of Remission in Active Ulcerative Colitis: A Randomized, Double-Blinded, Placebo-Controlled Multicenter Trial. Dig. Endosc. 2016, 28, 67–74..
Not in our library10.1111/den.12553
236.
Prebiotics, Probiotics, Synbiotics, Paraprobiotics and Postbiotic Compounds in IBD · 2021
No notice
237.
Glassner K. L.; Abraham B. P.; Quigley E. M. M. The Microbiome and Inflammatory Bowel Disease. J. Allergy Clin. Immunol. 2020, 145, 16–27..
Not in our library10.1016/j.jaci.2019.11.003
238.
Association between Faecalibacterium prausnitzii Reduction and Inflammatory Bowel Disease: A Meta-Analysis and Systematic Review of the Literature · 2014
No notice
239.
Zhao H.; Xu H.; Chen S.; He J.; Zhou Y.; Nie Y. Systematic Review and Meta-Analysis of the Role of Faecalibacterium Prausnitzii Alteration in Inflammatory Bowel Disease. J. Gastroenterol. Hepatol. 2021, 36, 320–328..
Not in our library10.1111/jgh.15222
240.
Qiu X.; Zhang M.; Yang X.; Hong N.; Yu C. Faecalibacterium Prausnitzii Upregulates Regulatory T Cells and Anti-Inflammatory Cytokines in Treating Tnbs-Induced Colitis. J. Crohns Colitis 2013, 7, e558–e568..
Not in our library10.1016/j.crohns.2013.04.002
241.
Martín R.; Chain F.; Miquel S.; Lu J.; Gratadoux J.-J.; Sokol H.; Verdu E. F.; Bercik P.; Bermúdez-Humarán L. G.; Langella P. The Commensal Bacterium Faecalibacterium Prausnitzii Is Protective in Dnbs-Induced Chronic Moderate and Severe Colitis Models. Inflamm. Bowel Dis. 2014, 20, 417–430..
Not in our library10.1097/01.mib.0000440815.76627.64
242.
He X.; Zhao S.; Li Y. Faecalibacterium Prausnitzii: A Next-Generation Probiotic in Gut Disease Improvement. Can. J. Infect. Dis. Med. Microbiol. 2021, 2021, 6666114.
Not in our library10.1155/2021/6666114
243.
Sokol H.; Leducq V.; Aschard H.; Pham H.-P.; Jegou S.; Landman C.; Cohen D.; Liguori G.; Bourrier A.; Nion-Larmurier I.; et al. Fungal Microbiota Dysbiosis in Ibd. Gut 2017, 66, 1039.
Not in our library10.1136/gutjnl-2015-310746
244.
Limon J. J.; Tang J.; Li D.; Wolf A. J.; Michelsen K. S.; Funari V.; Gargus M.; Nguyen C.; Sharma P.; Maymi V. I.; et al. Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models. Cell Host Microbe 2019, 25, 377–388..
Not in our library10.1016/j.chom.2019.01.007
245.
Norman J. M.; Handley S. A.; Baldridge M. T.; Droit L.; Liu C. Y.; Keller B. C.; Kambal A.; Monaco C. L.; Zhao G.; Fleshner P.; et al. Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease. Cell 2015, 160, 447–460..
Not in our library10.1016/j.cell.2015.01.002
246.
Kelesidis T.; Pothoulakis C. Efficacy and Safety of the Probiotic Saccharomyces Boulardii for the Prevention and Therapy of Gastrointestinal Disorders. Therap. Adv. Gastroenterol. 2012, 5, 111–125..
Not in our library10.1177/1756283x11428502
247.
Myles I. A.; Williams K. W.; Reckhow J. D.; Jammeh M. L.; Pincus N. B.; Sastalla I.; Saleem D.; Stone K. D.; Datta S. K. Transplantation of Human Skin Microbiota in Models of Atopic Dermatitis. JCI Insight 2016, 1, e86955.
Not in our library10.1172/jci.insight.86955
248.
Myles I. A.; Castillo C. R.; Barbian K. D.; Kanakabandi K.; Virtaneva K.; Fitzmeyer E.; Paneru M.; Otaizo-Carrasquero F.; Myers T. G.; Markowitz T. E.; et al. Therapeutic Responses to Roseomonas Mucosa in Atopic Dermatitis May Involve Lipid-Mediated Tnf-Related Epithelial Repair. Sci. Transl. Med. 2020, 12, eaaz8631.
Not in our library10.1126/scitranslmed.aaz8631
249.
Gupta K.; Stapleton A. E.; Hooton T. M.; Roberts P. L.; Fennell C. L.; Stamm W. E. Inverse Association of H2o2-Producing Lactobacilli and Vaginal Escherichia Coli Colonization in Women with Recurrent Urinary Tract Infections. J. Infect. Dis. 1998, 178, 446–450..
Not in our library10.1086/515635
250.
Kwok L.; Stapleton A. E.; Stamm W. E.; Hillier S. L.; Wobbe C. L.; Gupta K. Adherence of Lactobacillus Crispatus to Vaginal Epithelial Cells from Women with or without a History of Recurrent Urinary Tract Infection. J. Urol. 2006, 176, 2050–2054..
Not in our library10.1016/j.juro.2006.07.014
251.
Stapleton A. E.; Au-Yeung M.; Hooton T. M.; Fredricks D. N.; Roberts P. L.; Czaja C. A.; Yarova-Yarovaya Y.; Fiedler T.; Cox M.; Stamm W. E. Randomized, Placebo-Controlled Phase 2 Trial of a Lactobacillus Crispatus Probiotic Given Intravaginally for Prevention of Recurrent Urinary Tract Infection. Clin. Infect. Dis. 2011, 52, 1212–1217..
Not in our library10.1093/cid/cir183
252.
Sanders M. E.; Merenstein D. J.; Reid G.; Gibson G. R.; Rastall R. A. Probiotics and Prebiotics in Intestinal Health and Disease: From Biology to the Clinic. Nat. Rev. Gastroenterol. Hepatol. 2019, 16, 605–616..
Not in our library10.1038/s41575-019-0173-3
253.
Macfarlane S.; Macfarlane G. T.; Cummings J. H. Review Article: Prebiotics in the Gastrointestinal Tract. Aliment Pharmacol Ther. 2006, 24, 701–714..
Not in our library10.1111/j.1365-2036.2006.03042.x
254.
Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) Increase Bifidobacterium but Reduce Butyrate Producing Bacteria with Adverse Glycemic Metabolism in healthy young population · 2017
No notice
255.
Tandon D.; Haque M. M.; Gote M.; Jain M.; Bhaduri A.; Dubey A. K.; Mande S. S. A Prospective Randomized, Double-Blind, Placebo-Controlled, Dose-Response Relationship Study to Investigate Efficacy of Fructo-Oligosaccharides (Fos) on Human Gut Microflora. Sci. Rep. 2019, 9, 5473.
Not in our library10.1038/s41598-019-41837-3
256.
Finegold S. M.; Li Z.; Summanen P. H.; Downes J.; Thames G.; Corbett K.; Dowd S.; Krak M.; Heber D. Xylooligosaccharide Increases Bifidobacteria but Not Lactobacilli in Human Gut Microbiota. Food Funct. 2014, 5, 436–445..
Not in our library10.1039/c3fo60348b
257.
Björkstén B.; Sepp E.; Julge K.; Voor T.; Mikelsaar M. Allergy Development and the Intestinal Microflora During the First Year of Life. J. Allergy. Clin. Immunol. 2001, 108, 516–520..
Not in our library10.1067/mai.2001.118130
258.
Moro G.; Arslanoglu S.; Stahl B.; Jelinek J.; Wahn U.; Boehm G. A Mixture of Prebiotic Oligosaccharides Reduces the Incidence of Atopic Dermatitis During the First Six Months of Age. Arch. Dis. Child 2006, 91, 814–819..
Not in our library10.1136/adc.2006.098251
259.
Arslanoglu S.; Moro G. E.; Schmitt J.; Tandoi L.; Rizzardi S.; Boehm G. Early Dietary Intervention with a Mixture of Prebiotic Oligosaccharides Reduces the Incidence of Allergic Manifestations and Infections During the First Two Years of Life. J. Nut. 2008, 138, 1091–1095..
Not in our library10.1093/jn/138.6.1091
260.
Lindsay J. O.; Whelan K.; Stagg A. J.; Gobin P.; Al-Hassi H. O.; Rayment N.; Kamm M. A.; Knight S. C.; Forbes A. Clinical, Microbiological, and Immunological Effects of Fructo-Oligosaccharide in Patients with Crohn’s Disease. Gut 2006, 55, 348–355..
Not in our library10.1136/gut.2005.074971
261.
Han K.; Nam J.; Xu J.; Sun X.; Huang X.; Animasahun O.; Achreja A.; Jeon J. H.; Pursley B.; Kamada N.; et al. Generation of Systemic Antitumour Immunity Via the in Situ Modulation of the Gut Microbiome by an Orally Administered Inulin Gel. Nat. Biomed. Eng. 2021, 5, 1377–1388..
Not in our library10.1038/s41551-021-00749-2
262.
Routy B.; Le Chatelier E.; Derosa L.; Duong C. P. M.; Alou M. T.; Daillère R.; Fluckiger A.; Messaoudene M.; Rauber C.; Roberti M. P.; et al. Gut Microbiome Influences Efficacy of Pd-1–Based Immunotherapy against Epithelial Tumors. Science 2018, 359, 91–97..
Not in our library10.1126/science.aan3706
263.
Gopalakrishnan V.; Spencer C. N.; Nezi L.; Reuben A.; Andrews M. C.; Karpinets T. V.; Prieto P. A.; Vicente D.; Hoffman K.; Wei S. C.; et al. Gut Microbiome Modulates Response to Anti–Pd-1 Immunotherapy in Melanoma Patients. Science 2018, 359, 97–103..
Not in our library10.1126/science.aan4236
264.
Matson V.; Fessler J.; Bao R.; Chongsuwat T.; Zha Y.; Alegre M.-L.; Luke J. J.; Gajewski T. F. The Commensal Microbiome Is Associated with Anti–Pd-1 Efficacy in Metastatic Melanoma Patients. Science 2018, 359, 104–108..
Not in our library10.1126/science.aao3290
265.
Dethlefsen L.; Relman D. A. Incomplete Recovery and Individualized Responses of the Human Distal Gut Microbiota to Repeated Antibiotic Perturbation. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 4554–4561..
Not in our library10.1073/pnas.1000087107
266.
Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances · 2016
No notice
267.
Raymond F.; Ouameur A. A.; Déraspe M.; Iqbal N.; Gingras H.; Dridi B.; Leprohon P.; Plante P.-L.; Giroux R.; Bérubé È.; et al. The Initial State of the Human Gut Microbiome Determines Its Reshaping by Antibiotics. ISME J. 2016, 10, 707–720..
Not in our library10.1038/ismej.2015.148
268.
Vickers R. J.; Tillotson G.; Goldstein E. J. C.; Citron D. M.; Garey K. W.; Wilcox M. H. Ridinilazole: A Novel Therapy for Clostridium Difficile Infection. Int. J. Antimicrob. Agents 2016, 48, 137–143..
Not in our library10.1016/j.ijantimicag.2016.04.026
269.
Vickers R. J.; Tillotson G. S.; Nathan R.; Hazan S.; Pullman J.; Lucasti C.; Deck K.; Yacyshyn B.; Maliakkal B.; Pesant Y.; et al. Efficacy and Safety of Ridinilazole Compared with Vancomycin for the Treatment of Clostridium Difficile Infection: A Phase 2, Randomised, Double-Blind, Active-Controlled, Non-Inferiority Study. Lancet Infect. Dis. 2017, 17, 735–744..
Not in our library10.1016/s1473-3099(17)30235-9
270.
Thorpe C. M.; Kane A. V.; Chang J.; Tai A.; Vickers R. J.; Snydman D. R. Enhanced Preservation of the Human Intestinal Microbiota by Ridinilazole, a Novel Clostridium Difficile-Targeting Antibacterial, Compared to Vancomycin. PLoS One 2018, 13, e0199810.
Not in our library10.1371/journal.pone.0199810
271.
Avis T.; Wilson F. X.; Khan N.; Mason C. S.; Powell D. J. Targeted Microbiome-Sparing Antibiotics. Drug Discovery 2021, 26, 2198–2203..
Not in our library10.1016/j.drudis.2021.07.016
272.
Machado A.; Cerca N. Influence of Biofilm Formation by Gardnerella Vaginalis and Other Anaerobes on Bacterial Vaginosis. J. Infect. Dis. 2015, 212, 1856–1861..
Not in our library10.1093/infdis/jiv338
273.
Bradshaw C. S.; Sobel J. D. Current Treatment of Bacterial Vaginosis—Limitations and Need for Innovation. J. Infect. Dis. 2016, 214, S14–S20..
Not in our library10.1093/infdis/jiw159
274.
Landlinger C.; Tisakova L.; Oberbauer V.; Schwebs T.; Muhammad A.; Latka A.; Van Simaey L.; Vaneechoutte M.; Guschin A.; Resch G.; et al. Engineered Phage Endolysin Eliminates Gardnerella Biofilm without Damaging Beneficial Bacteria in Bacterial Vaginosis Ex Vivo. Pathogens 2021, 10, 54.
Not in our library10.3390/pathogens10010054
275.
Whitney C. G.; Farley M. M.; Hadler J.; Harrison L. H.; Bennett N. M.; Lynfield R.; Reingold A.; Cieslak P. R.; Pilishvili T.; Jackson D.; et al. Decline in Invasive Pneumococcal Disease after the Introduction of Protein–Polysaccharide Conjugate Vaccine. N. Engl. J. Med. 2003, 348, 1737–1746..
Not in our library10.1056/nejmoa022823
276.
Biesbroek G.; Wang X.; Keijser B. J.; Eijkemans R. M.; Trzciński K.; Rots N. Y.; Veenhoven R. H.; Sanders E. A.; Bogaert D. Seven-Valent Pneumococcal Conjugate Vaccine and Nasopharyngeal Microbiota in Healthy Children. Emerg. Infect. Dis. 2014, 20, 201–210..
Not in our library10.3201/eid2002.131220
277.
Blaser M. J.; Falkow S. What Are the Consequences of the Disappearing Human Microbiota?. Nat. Rev. Microbiol. 2009, 7, 887–894..
Not in our library10.1038/nrmicro2245
278.
Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study · 2017
Not checked
279.
Relman D. A.; Lipsitch M. Microbiome as a Tool and a Target in the Effort to Address Antimicrobial Resistance. Proc. Natl. Acad. Sci. U.S.A. 2018, 115, 12902–12910..
Not in our library10.1073/pnas.1717163115
280.
Brown R.; Lengeling A.; Wang B. Phage Engineering: How Advances in Molecular Biology and Synthetic Biology Are Being Utilized to Enhance the Therapeutic Potential of Bacteriophages. Quant. Biol. 2017, 5, 42–54..
Not in our library10.1007/s40484-017-0094-5
281.
Zhang Y.; Li C.-X.; Zhang X.-Z. Bacteriophage-Mediated Modulation of Microbiota for Diseases Treatment. Adv. Drug Delivery Rev. 2021, 176, 113856.
Not in our library10.1016/j.addr.2021.113856
282.
Duan Y.; Llorente C.; Lang S.; Brandl K.; Chu H.; Jiang L.; White R. C.; Clarke T. H.; Nguyen K.; Torralba M.; et al. Bacteriophage Targeting of Gut Bacterium Attenuates Alcoholic Liver Disease. Nature 2019, 575, 505–511..
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283.
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Ultrasound-controllable engineered bacteria for cancer immunotherapy · 2022
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318.
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Interplay between the human gut microbiome and host metabolism · 2019
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The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication · 2020
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332.
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333.
Evidence for the Gut Microbiota Short-Chain Fatty Acids as Key Pathophysiological Molecules Improving Diabetes · 2014
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349.
The Super-Donor Phenomenon in Fecal Microbiota Transplantation · 2019
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350.
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351.
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Hofer U. The Next Step Towards Anticancer Microbiota Therapeutics. Nature Rev. Microbiol. 2019, 17, 125–125..
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Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis · 2021
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356.
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases · 2019
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362.
The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease · 2014
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Not in our library10.1038/s41592-018-0301-y
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Tridgett M.; Ababi M.; Osgerby A.; Ramirez Garcia R.; Jaramillo A. Engineering Bacteria to Produce Pure Phage-Like Particles for Gene Delivery. ACS Synth. Biol. 2021, 10, 107–114..
Not in our library10.1021/acssynbio.0c00467
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Not in our library10.1016/j.jconrel.2020.06.016
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Phage-mediated horizontal gene transfer and its implications for the human gut microbiome · 2022
No notice
481.
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Cited by papers we hold 1

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation · 2024
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