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Characterization of the urogenital microbiome in patients with urinary tract infections

Indonesian Journal of Biotechnology · Vol. 27 No. 3 (2022) · pp. 142–150

DOI
10.22146/ijbiotech.69212
ISSN
2089-2241, 0853-8654
Published
2022-09-30
Publisher
Universitas Gadjah Mada
Language
eng
License
creativecommons.org/licenses/by-sa/4.0

Abstract

Standard microbiological culture techniques can only identify a fraction of the urogenital microbiome. Meanwhile, identifying and characterizing infectious microorganisms are very important for the success of diagnosis and treatments, especially for Urinary Tract Infection (UTI) patients. This study aimed to characterize the urogenital microbiome of UTI patients using 16S rRNA gene sequencing. We sequenced two pooled DNA samples from voided urine of UTI patients (21 females and 13 males). To determine the structure and composition of taxa in the samples, 16S rRNA gene sequencing was performed using the Illumina Mi‐Seq paired‐end platform. The most abundant genera were Burkholderia‐Caballeronia‐Paraburkholderia (71%) followed by Prevotella (33%), Escherichia‐Shigella (24%), Klebsiella (23%) and Sneathia (10%). The female microbiome was dominated by Prevotella bivia (28%), Escherichia coli (24%), Sneathia sanguinegens (7%) and Klebsiella pneumoniae (4%). On the other hand, the male microbiome was dominated by K. pneumoniae (23%) and E. coli (2%). K. pneumoniae and E. coli were the most abundant species found in both microbiomes. The 16S rRNA gene sequencing used in this study successfully uncovered the composition of the urogenital microbiome, which might not have been possible with conventional culture methods.

Keywords

Collaboration network of the authors

40 authors · 145 co-authorship links · showing the 40 most connected

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  • University of Palangka Raya
  • Universitas Gadjah Mada
  • State University of Jakarta
  • Affiliation unknown
  • Different organisations
  • Same organisation
  • Affiliation unknown
  • Thicker line = more joint articles · bigger circle = more articles
Show as table
Co-authorOrganisationJoint articles
Purnomo PurnomoAffiliation unknown5
Arif muazamAffiliation unknown2
Setyorini WidyayantiAffiliation unknown2
Adib Fakhruddin YusufAffiliation unknown2
Wahyu WilopoAffiliation unknown2
Adventus PandaUniversity of Palangka Raya2
Dwi PriyowidodoAffiliation unknown2
Tjut Sugandawaty DjohanAffiliation unknown2
Ganies Riza AristyaAffiliation unknown2
Tuty ArisuryantiAffiliation unknown2
Laurentius Hartanto NugrohoAffiliation unknown2
KEIKO T. NATSUAKIAffiliation unknown2
Eko Agus SuyonoAffiliation unknown2
sukirno sukirnoAffiliation unknown2
Yekti Asih PurwestriAffiliation unknown2
Suharyanto SuharyantoUniversitas Gadjah Mada1
Uni Baroroh HusnudinAffiliation unknown1
Rizal Hermawan SetiyobudiAffiliation unknown1
Lies Mira YusiatiAffiliation unknown1
Widodo WidodoState University of Jakarta1
Asih KurniawatiAffiliation unknown1
Ketut Arte WidaneAffiliation unknown1
Annisaa WidyasariAffiliation unknown1
Bernardinus PratamaAffiliation unknown1
Ari MeididitAffiliation unknown1
Okta SimonAffiliation unknown1
Karmilah KarmilahAffiliation unknown1
Vida Rahma LatifahAffiliation unknown1
Vivi Indah NurcahyatiAffiliation unknown1
Anggun Diyan NurhasanahAffiliation unknown1
Adristi Shafa WidyasariAffiliation unknown1
Ananto Puradi NainggolanAffiliation unknown1
Aldy Riau Wansyah HasibuanAffiliation unknown1
Madyan Akmal HidayatAffiliation unknown1
Arini Dian PratiwiAffiliation unknown1
Rindu AurantikaAffiliation unknown1

Affiliations come from OpenAlex; journal OAI-PMH metadata carries none. Authors without an OpenAlex ID are matched by name, which can merge or split people.

Metadata source: OAI-PMH (metadata jurnal) https://jurnal.ugm.ac.id/ijbiotech/oai, first harvested 8 Nov 2026, last seen 8 Nov 2026.
Original metadata (oai_dc) 
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	<dc:title xml:lang="en-US">Characterization of the urogenital microbiome in patients with urinary tract infections</dc:title>
	<dc:creator>Nadifah, Fitri</dc:creator>
	<dc:creator>Artama, Wayan Tunas</dc:creator>
	<dc:creator>Daryono, Budi Setiadi</dc:creator>
	<dc:creator>Retnaningrum, Endah</dc:creator>
	<dc:subject xml:lang="en-US">urogenital microbiome; UTIs; 16S rRNA sequencing; bacteria</dc:subject>
	<dc:description xml:lang="en-US">Standard microbiological culture techniques can only identify a fraction of the urogenital microbiome. Meanwhile, identifying and characterizing infectious microorganisms are very important for the success of diagnosis and treatments, especially for Urinary Tract Infection (UTI) patients. This study aimed to characterize the urogenital microbiome of UTI patients using 16S rRNA gene sequencing. We sequenced two pooled DNA samples from voided urine of UTI patients (21 females and 13 males). To determine the structure and composition of taxa in the samples, 16S rRNA gene sequencing was performed using the Illumina Mi‐Seq paired‐end platform. The most abundant genera were Burkholderia‐Caballeronia‐Paraburkholderia (71%) followed by Prevotella (33%), Escherichia‐Shigella (24%), Klebsiella (23%) and Sneathia (10%). The female microbiome was dominated by Prevotella bivia (28%), Escherichia coli (24%), Sneathia sanguinegens (7%) and Klebsiella pneumoniae (4%). On the other hand, the male microbiome was dominated by K. pneumoniae (23%) and E. coli (2%). K. pneumoniae and E. coli were the most abundant species found in both microbiomes. The 16S rRNA gene sequencing used in this study successfully uncovered the composition of the urogenital microbiome, which might not have been possible with conventional culture methods.</dc:description>
	<dc:publisher xml:lang="en-US">Universitas Gadjah Mada</dc:publisher>
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	<dc:date>2022-09-30</dc:date>
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	<dc:identifier>https://journal.ugm.ac.id/ijbiotech/article/view/69212</dc:identifier>
	<dc:identifier>10.22146/ijbiotech.69212</dc:identifier>
	<dc:source xml:lang="en-US">Indonesian Journal of Biotechnology; Vol 27, No 3 (2022); 142-150</dc:source>
	<dc:source>2089-2241</dc:source>
	<dc:source>0853-8654</dc:source>
	<dc:language>eng</dc:language>
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	<dc:rights xml:lang="en-US">Copyright (c) 2022 The Author(s)</dc:rights>
	<dc:rights xml:lang="en-US">http://creativecommons.org/licenses/by-sa/4.0</dc:rights>
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