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Article ; Online: Using unsupervised machine learning to classify behavioral risk markers of bacterial vaginosis.

Rodriguez, Violeta J / Pan, Yue / Salazar, Ana S / Nogueira, Nicholas Fonseca / Raccamarich, Patricia / Klatt, Nichole R / Jones, Deborah L / Alcaide, Maria L

Archives of gynecology and obstetrics

2024 Volume 309, Issue 3, Page(s) 1053–1063

Abstract: Introduction: This study used an unsupervised machine learning algorithm, sidClustering and random forests, to identify clusters of risk behaviors of Bacterial Vaginosis (BV), the most common cause of abnormal vaginal discharge linked to STI and HIV ... ...

Abstract	Introduction: This study used an unsupervised machine learning algorithm, sidClustering and random forests, to identify clusters of risk behaviors of Bacterial Vaginosis (BV), the most common cause of abnormal vaginal discharge linked to STI and HIV acquisition. METHODS: Participants were 391 cisgender women in Miami, Florida, with a mean of 30.8 (SD = 7.81) years of age; 41.7% identified as Hispanic; 41.7% as Black and 44.8% as White. Participants completed measures of demographics, risk behaviors [sexual, medical, and reproductive history, substance use, and intravaginal practices (IVP)], and underwent collection of vaginal samples; 135 behavioral variables were analyzed. BV was diagnosed using Nugent criteria. Results: We identified four clusters, and variables were ranked by importance in distinguishing clusters: Cluster 1: nulliparous women who engaged in IVPs to clean themselves and please sexual partners, and used substances frequently [n = 118 (30.2%)]; Cluster 2: primiparous women who engaged in IVPs using vaginal douches to clean themselves (n = 112 (28.6%)]; Cluster 3: primiparous women who did not use IVPs or substances [n = 87 (22.3%)]; and Cluster 4: nulliparous women who did not use IVPs but used substances [n = 74 (18.9%)]. Clusters were related to BV (p < 0.001). Cluster 2, the cluster of women who used vaginal douches as IVPs, had the highest prevalence of BV (52.7%). Conclusions: Machine learning methods may be particularly useful in identifying specific clusters of high-risk behaviors, in developing interventions intended to reduce BV and IVP, and ultimately in reducing the risk of HIV infection among women.
MeSH term(s)	Female ; Humans ; Vaginosis, Bacterial/diagnosis ; Vaginosis, Bacterial/epidemiology ; Vaginosis, Bacterial/microbiology ; HIV Infections/diagnosis ; HIV Infections/epidemiology ; HIV Infections/complications ; Unsupervised Machine Learning ; Vagina/microbiology ; Sexual Behavior
Language	English
Publishing date	2024-02-03
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	896455-5
ISSN	1432-0711 ; 0932-0067
ISSN (online)	1432-0711
ISSN	0932-0067
DOI	10.1007/s00404-023-07360-7
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Article ; Online: Probiotic Therapy During Vaccination Alters Antibody Response to Simian-Human Immunodeficiency Virus Infection But Not to Commensals.

Wilson, Andrew / Manuzak, Jennifer A / Liang, Hua / Leda, Ana R / Klatt, Nichole / Lynch, Rebecca M

AIDS research and human retroviruses

2023 Volume 39, Issue 5, Page(s) 222–231

Abstract: The induction of robust circulating antibody titers is a key goal of HIV-1 vaccination. Probiotic supplementation is an established strategy to enhance microbiota and boost antibody responses to vaccines. A recent study tested whether oral probiotics ... ...

Abstract	The induction of robust circulating antibody titers is a key goal of HIV-1 vaccination. Probiotic supplementation is an established strategy to enhance microbiota and boost antibody responses to vaccines. A recent study tested whether oral probiotics could enhance vaccine-specific mucosal immunity by testing vaccination with and without supplementation in a Rhesus macaque Simian-Human Immunodeficiency Virus challenge model. Although supplementation was not associated with protection, the effects of probiotics on immunity after infection were not examined. To address this question, we measured antibody titers to HIV Env and commensal bacteria in plasma from the vaccination/supplementation time points as well as after Simian-Human Immunodeficiency Virus (SHIV) acquisition. We found that a trend toward lower HIV Env-specific titers in the animals given probiotics plus vaccine became greater after SHIV infection. Significantly lower Immunoglobulin (Ig) A titers were observed in animals vaccinated and supplemented compared with vaccine alone due to a delay in antibody kinetics at week 2 postinfection. We observed no difference, however, in titers to commensal bacteria during probiotic supplementation or after SHIV infection. These results suggest that probiotic supplementation may be a strategy for reducing IgA-specific HIV antibodies in the plasma, a correlate associated with increased HIV infection in the RV144 clinical trial.
MeSH term(s)	Animals ; Humans ; HIV Infections/prevention & control ; Antibody Formation ; Macaca mulatta ; Simian Immunodeficiency Virus ; Vaccination ; HIV-1 ; Simian Acquired Immunodeficiency Syndrome/prevention & control ; AIDS Vaccines
Chemical Substances	AIDS Vaccines
Language	English
Publishing date	2023-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	639130-8
ISSN	1931-8405 ; 0889-2229
ISSN (online)	1931-8405
ISSN	0889-2229
DOI	10.1089/AID.2022.0123
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Article ; Online: Microbial Effects on Immunity in HIV: Virus, Gender or Sexual Preference Induced?

Klatt, Nichole R / Manuzak, Jennifer A

EBioMedicine

2018 Volume 31, Page(s) 7–8

MeSH term(s)	HIV ; Humans ; Microbiota ; Sexual Behavior ; Sexual Partners
Language	English
Publishing date	2018-04-07
Publishing country	Netherlands
Document type	Journal Article ; Comment
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2018.04.008
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Article ; Online: MicroRNAs: novel tools to block gut inflammation in HIV?

Klatt, Nichole R / Hunt, Peter W

AIDS (London, England)

2017 Volume 31, Issue 14, Page(s) 2017–2018

MeSH term(s)	HIV Infections ; Humans ; Inflammation ; Intestinal Mucosa ; MicroRNAs
Chemical Substances	MicroRNAs
Language	English
Publishing date	2017-08-30
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	639076-6
ISSN	1473-5571 ; 0269-9370 ; 1350-2840
ISSN (online)	1473-5571
ISSN	0269-9370 ; 1350-2840
DOI	10.1097/QAD.0000000000001609
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Article ; Online: Timothy Ray Brown: The Serendipitous Hero of HIV Cure Research.

Hope, Thomas J / Klatt, Nichole R / Sacha, Jonah B / Cannon, Paula M

AIDS research and human retroviruses

2020 Volume 36, Issue 11, Page(s) 883–885

Language	English
Publishing date	2020-10-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	639130-8
ISSN	1931-8405 ; 0889-2229
ISSN (online)	1931-8405
ISSN	0889-2229
DOI	10.1089/AID.2020.0253
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Article ; Online: Gender Identity Stigma in Transgender Women Is Higher After Gender-Affirming Vaginoplasty.

Fein, Lydia A / Barnett, Rebecca / Liu, Tianhao / Potter, JoNell E / Klatt, Nichole R / Alcaide, Maria L / Jones, Deborah L

AIDS research and human retroviruses

2023

Abstract: Gender affirmation may reduce stigma and gender-based discrimination that drive increased behaviors that can lead to HIV in transgender women (TW). For many TW, vaginoplasty is gender affirming, yet has not been previously evaluated with regard to ... ...

Abstract	Gender affirmation may reduce stigma and gender-based discrimination that drive increased behaviors that can lead to HIV in transgender women (TW). For many TW, vaginoplasty is gender affirming, yet has not been previously evaluated with regard to likelihood of HIV. This pilot study of TW aimed to evaluate the influence of gender-affirming vaginoplasty on stigma and the drivers of HIV acquisition. Adult TW without HIV were recruited. Interviewer-administered surveys were used to assess demographics, gender identity stigma, psychosocial factors, importance of and satisfaction with gender affirmation, and behaviors that increase the likelihood of HIV in TW who had either undergone gender-affirming vaginoplasty (TWWV) or who had not (TWWOV). Statistical analysis was conducted using descriptive statistics, Fisher's exact tests, and Wilcoxon rank-sum tests. Thirty TW without HIV (19-83 years old) participated (TWWV = 10; TWWOV = 20). The majority identified with ethnic minority groups (
Language	English
Publishing date	2023-12-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	639130-8
ISSN	1931-8405 ; 0889-2229
ISSN (online)	1931-8405
ISSN	0889-2229
DOI	10.1089/AID.2023.0017
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Article ; Online: Problematic Cannabis Use Is Associated with Reduced Rectal Microbial Species Richness and Diversity Among a Pilot Sample of Young Sexual and Gender Minorities.

Morgan, Ethan / Manuzak, Jennifer A / Broedlow, Courtney / Hudson, Hannah / D'Aquila, Richard / Carrico, Adam W / Klatt, Nichole R / Mustanski, Brian

AIDS research and human retroviruses

2023 Volume 40, Issue 1, Page(s) 1–6

Abstract: Compared to young heterosexual men, young sexual and gender minorities (YSGM) have elevated systemic inflammation and unique intestinal microbial profiles, influenced by HIV infection and substance use. However, links between cannabis use and microbial ... ...

Abstract	Compared to young heterosexual men, young sexual and gender minorities (YSGM) have elevated systemic inflammation and unique intestinal microbial profiles, influenced by HIV infection and substance use. However, links between cannabis use and microbial dysbiosis in this population have not been well described. In this pilot study, we aimed to characterize the complex interrelationships between cannabis use and microbial community structure in YSGM in relationship to HIV status. Cannabis use was assessed by self-administered Cannabis Use Disorder Identification Test (CUDIT) questionnaires and rectal microbial community alpha-diversity metrics were assessed via 16S ribosomal ribonucleic acid (rRNA) sequencing in a subset of YSGM (
MeSH term(s)	Humans ; Male ; HIV Infections/epidemiology ; Cannabis/genetics ; Pilot Projects ; Sexual and Gender Minorities ; Substance-Related Disorders ; Inflammation ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	639130-8
ISSN	1931-8405 ; 0889-2229
ISSN (online)	1931-8405
ISSN	0889-2229
DOI	10.1089/aid.2022.0143
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Article ; Online: Microbial mismanagement: how inadequate treatments for vaginal dysbiosis drive the HIV epidemic in women.

Gustin, Andrew / Cromarty, Ross / Schifanella, Luca / Klatt, Nichole R

Seminars in immunology

2021 Volume 51, Page(s) 101482

Abstract: Women and girls represent a key population driving new HIV infections and persistence of the HIV pandemic. A key determinant of HIV susceptibility is the composition of the vaginal microbiome, which can influence the local immune cell population, ... ...

Abstract	Women and girls represent a key population driving new HIV infections and persistence of the HIV pandemic. A key determinant of HIV susceptibility is the composition of the vaginal microbiome, which can influence the local immune cell population, inflammation status, and HIV prevention drug levels. While a low-diversity composition dominated by Lactobacillus crispatus is associated with a decreased risk of HIV acquisition, high diversity environments associated with bacterial vaginosis increase risk of HIV. Given the important role of the vaginal microbiome in determining HIV susceptibility, altering the microbiome towards a Lactobacillus-dominated state is an attractive complementary strategy to reduce HIV incidence rates. Here, we provide an overview of the mechanisms by which the vaginal microbiome may contribute to HIV acquisition risk. Furthermore, we address the advantages and limitations of historical treatments and emerging technologies under investigation to modify the vaginal microbiome, including: antibiotics, bacteriophages, probiotics, topicals, and engineered bacteria. By addressing the current state of vaginal microbiome knowledge and strategies for manipulation, we hope to amplify the growing calls for increased resources and research into vaginal microbial health, which will be essential to accelerating preventative efforts amongst the world's most vulnerable populations.
MeSH term(s)	Dysbiosis ; Female ; HIV Infections/epidemiology ; HIV Infections/therapy ; Humans ; Microbiota ; Vagina/microbiology ; Vaginosis, Bacterial/epidemiology ; Vaginosis, Bacterial/microbiology ; Vaginosis, Bacterial/therapy
Language	English
Publishing date	2021-06-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1018141-6
ISSN	1096-3618 ; 1044-5323
ISSN (online)	1096-3618
ISSN	1044-5323
DOI	10.1016/j.smim.2021.101482
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Article ; Online: Accommodating multiple potential normalizations in microbiome associations studies.

Song, Hoseung / Ling, Wodan / Zhao, Ni / Plantinga, Anna M / Broedlow, Courtney A / Klatt, Nichole R / Hensley-McBain, Tiffany / Wu, Michael C

BMC bioinformatics

2023 Volume 24, Issue 1, Page(s) 22

Abstract: Background: Microbial communities are known to be closely related to many diseases, such as obesity and HIV, and it is of interest to identify differentially abundant microbial species between two or more environments. Since the abundances or counts of ... ...

Abstract	Background: Microbial communities are known to be closely related to many diseases, such as obesity and HIV, and it is of interest to identify differentially abundant microbial species between two or more environments. Since the abundances or counts of microbial species usually have different scales and suffer from zero-inflation or over-dispersion, normalization is a critical step before conducting differential abundance analysis. Several normalization approaches have been proposed, but it is difficult to optimize the characterization of the true relationship between taxa and interesting outcomes. RESULTS: To avoid the challenge of picking an optimal normalization and accommodate the advantages of several normalization strategies, we propose an omnibus approach. Our approach is based on a Cauchy combination test, which is flexible and powerful by aggregating individual p values. We also consider a truncated test statistic to prevent substantial power loss. We experiment with a basic linear regression model as well as recently proposed powerful association tests for microbiome data and compare the performance of the omnibus approach with individual normalization approaches. Experimental results show that, regardless of simulation settings, the new approach exhibits power that is close to the best normalization strategy, while controling the type I error well. CONCLUSIONS: The proposed omnibus test releases researchers from choosing among various normalization methods and it is an aggregated method that provides the powerful result to the underlying optimal normalization, which requires tedious trial and error. While the power may not exceed the best normalization, it is always much better than using a poor choice of normalization.
MeSH term(s)	Microbiota ; Computer Simulation ; Linear Models ; Research
Language	English
Publishing date	2023-01-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-023-05147-w
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Article ; Online: PrEP awareness and use among reproductive age women in Miami, Florida.

Nogueira, Nicholas Fonseca / Luisi, Nicole / Salazar, Ana S / Cherenack, Emily M / Raccamarich, Patricia / Klatt, Nichole R / Jones, Deborah L / Alcaide, Maria L

PloS one

2023 Volume 18, Issue 6, Page(s) e0286071

Abstract: Background: Miami, Florida is an epicenter of the HIV epidemic in the US, with 20% of new HIV infections occurring in women. Despite effectiveness of Pre-Exposure Prophylaxis (PrEP) in preventing HIV, only 10% of eligible women benefit from its use.: ... ...

Abstract	Background: Miami, Florida is an epicenter of the HIV epidemic in the US, with 20% of new HIV infections occurring in women. Despite effectiveness of Pre-Exposure Prophylaxis (PrEP) in preventing HIV, only 10% of eligible women benefit from its use. Setting: This study evaluates PrEP awareness and use, and factors associated with PrEP awareness among sexually active women in Miami, Florida. Methods: Results reported in this study included cross-sectional data that were collected as part of a baseline visit from a parent study. Cis-gender, HIV-negative, 18-45-year-old, sexually active women were recruited as part of a study evaluating recurrent bacterial vaginosis and HIV risk. Participants completed questionnaires assessing socio-demographics, HIV risk factors, prior history of HIV testing and reproductive tract infections, PrEP awareness and use. Relationships between variables and PrEP awareness were analyzed and multivariable logistic regression identified variables strongly associated with PrEP awareness. Results: Among the 295 women enrolled, median age was 31 (24-38) years, 49% Black, 39% White, and 34% Hispanic. Of 63% who knew about PrEP, only 5% were on PrEP. Women with income below poverty line (OR = 2.00[1.04,3.87];p = 0.04), more male sexual partners in past month (OR = 1.30[1.01,1.68];p = 0.04), lifetime HIV testing (OR = 6.42[2.83,14.52];p<0.01), and current bacterial vaginosis (OR = 2.28[1.18,4.40];p = 0.01) were more likely to be aware of PrEP. Lower odds of PrEP awareness were associated with being Black (OR = 0.38[0.15,0.96];p = 0.04), Hispanic (OR = 0.18[0.08,0.39];p<0.01), heterosexual (OR = 0.29[0.11,0.77];p<0.01), and reporting inconsistent condom use during vaginal sex (OR = 0.21[0.08,0.56];p<0.01). Conclusion: PrEP awareness is low among reproductive age women in a high-risk setting. Culturally tailored interventions are needed to increase PrEP awareness and uptake, especially among Black and Hispanic women with inconsistent condom use during vaginal sex with male partners.
MeSH term(s)	Adolescent ; Adult ; Female ; Humans ; Middle Aged ; Young Adult ; Cross-Sectional Studies ; Florida/epidemiology ; Health Knowledge, Attitudes, Practice ; HIV Infections/epidemiology ; HIV Infections/prevention & control ; Homosexuality, Male ; Pre-Exposure Prophylaxis ; Sexual Partners ; Vaginosis, Bacterial
Language	English
Publishing date	2023-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0286071
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