Nostril and oropharyngeal bacterial microbiota based on 16S rRNA gene clone libraries. We also examined the microbiota of the nostril and oropharynx from four of the seven participants sampled using 16S rRNA gene clone libraries. The PhyloChip de- tects rare taxa that are unlikely to be detected in standard-sized clone libraries of 200 to 500 clones per sample, provided that there are probes for these taxa on the array. Clone libraries, however, permit direct identification of highly prevalent 16S rRNA gene sequences present in the sample. In total, from all four adults, we analyzed 719 nostril-derived clones and 666 oropharynx-derived clones. We detected 36 taxa (defined by clustering at 97% nucle- otide identity) from the nostrils and 71 taxa from the oropharynx (see Fig. S2A and B in the supplemental material). At 97%, the Chao 1 value (an estimate of community richness) for nostrils was 50 taxa (standard deviation ⫾ 7.2) and for the oropharynges 120 taxa (SD ⫾ 17). The 36 taxa present in the nostril samples clus- tered within five bacterial phyla: Actinobacteria, Firmicutes, Pro- teobacteria, Bacteroidetes, and Fusobacteria (in addition to chloro- plasts [see Fig. S2A in the supplemental material]). The 71 taxa detected in the oropharyngeal samples clustered within seven bac- terial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, Actinobacteria, TM7, and SR1 (see Fig. S2B). As stated above, the relative abundance of each phylum in each site was similar to that detected by the microarrays (Fig. 1 and see Fig. S2C in the supple- mental material). Rarefaction analysis demonstrated that at 97% sequence clustering, the combined libraries for each site were be- ginning to saturate (see Fig. S2D). This is best explained by the large proportion of rare taxa detected using the microarray (each present at ⬍0.05% of the estimated total 16S rRNA gene copy number based on hybridization signals, as shown in Fig. 4A), which are unlikely to appear within clone libraries of the size con- structed for this study.
preservative function only. Youn et al ’ s study shows that the above antifungal agents are effective to inhibit the growth of several Malassezia species including M. restricta and M. globose. 30 Despite the fungal component of the skin microbiota was not investigated in this study, it cannot be excluded that the bene ﬁ cial properties of piroctone olamine and climbazole may contribute to alleviating the SD symp- tomatology. The tested cream contains also of topical glycyr- rhetinic acid. Therapeutic potential of glycyrrhetinic acids was resumed in a patent review published not long ago. 31 Topical glycyrretinic acid exerts anti-in ﬂ ammatory action. 32 A shampoo with glycyrretinic acid was effective in the treat- ment of dandruff. 33 Finally, the cream contains a bacterial- wall-derived glycoproteins and peptide glycans complex which could exert an immunomodulator action 34 with a direct in ﬂ uence on the skin microbiome composition. In evaluating the results of our study, we must take into account some trial ’ s limitations. First, this was uncontrolled, not randomized trial. However, in order to reduce the investiga- tor bias, we adopted an assessor-blinded study design for the evaluation of the primary clinical end-point. In addition, the skin microbiota evaluation should be considered as an opera- tor-independent study outcome. Another study limitation was that we did not evaluate the modi ﬁ cation of yeast micro- biome. However, one of the main goals of our study was to con ﬁ rm or not the role of the bacterial population of the skin microbiota in SD. As stated before, in SD subjects, bacterial disequilibrium of skin microbiome seems to be more related to the severity of the disease than Malassezia spp. 16 Finally, our study was not a comparative trial (ie, a comparison with an antifungal product or a corticosteroid) and therefore is not possible to exclude that clinical ef ﬁ cacy of SD reference standard treatments could be associated with an improve- ment of skin bacterial microbiota. In this regards, future comparative trials are warranted. However, the main strength of our study was that for the ﬁ rst time we were able to demonstrate that a corticosteroid-free cream together with a signi ﬁ cant clinical positive effect was able to riequilibrate the facial skin bacterial microbiome.
19, paragraph 4). A recent study reported the existence of a microbiota associated to the bovine placenta, but the authors could not exclude a possible contamina- tion of the biopsies during sampling . Moreover, the extraction of the mentioned biopsies was done through the vaginal tract of the live cows exposing the samples to the commensal microbiota. Although the authors took care to apply antimicrobial solution before and between sampling, this does not ensure elimination of DNA which then may persist, e.g. leading to the reported presence of the phyla Planctomycetes, a slow-growing decomposer of organic matter  and Euyarchaeota, a methanogenic archaea group from the rumen of cattle  in the pla- centa and the amniotic fluid. A previous work showed for the first time the presence of prenatal microbiota in human placentas . However, a subsequent study concluded with a new sample set that the previous one could not distinguish between placental microbiota and contamination introduced during DNA purification . Our findings indicate that under timely and sterile sam- pling conditions, bacterial microbiota is likely absent from these tissues.
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A study was carried out to assess the colonization of bacterial strains adherent to the upper and lower sides of the mulberry leaves, in the intestinal zones of the silkworm Bombyx mori. Upper and lower sides of one week, two week and three week old mulberry leaves were scraped aseptically and cultured in nutrient agar medium. Morphological, physiological and fermentation characteristics of the bacterial isolates were studied to identify the strains. The bacterial strains isolated were: Bacillus cereus, Bacillus subtilis, Lactococcus lactis, Staphylococcus lactis, Enterobacter aerogenes, Escherichia coli Klebsiella pneumoniae. Second instar larvae of Bombyx mori were three sets and each set was maintained on mulberry leaves of selected age( one, two or three week old) for 15 days and the regionwise abundance of gut bacteria was assessed. Among the intestinal zones of Bombyx mori foregut harboured more bacteria ( 5.2
Some bacterial strains are able to produce insecticidal compounds that act like natural pesticides. The bacterium Bacillus thuringiensis serovar israelensis produces two dif- ferent toxins encoded by the cry and cyt genes located on a plasmid replicon . The Cry toxins act on a large in- sect spectrum (Coleoptera, Lepidoptera, Hymenoptera and Diptera), whereas the Cyt toxins act specifically on Diptera . Both toxins are activated by the alkaline pH of the larval gut and are able to degrade the midgut membrane causing larvae to die . The Firmicute Lysinibacillus sphaericus also contains the insecticidal Mtx and Bin toxins that are highly active against mosquito lar- vae . These toxins paralyze the digestive system and disrupt the insect nervous system. These two classes of larvicidal bacteria are major mosquitocidal candidates and were successfully used in the field to reduce An. gambiae populations responsible for malaria outbreaks in Gambia and Ghana [106,107]. Finally, larvicidal toxins of Clostrid- ium bifermentans serovar Malaysia and the pupicidal toxin of Bacillus subtilis subspecies subtilis are also potential candidates as agents in biological control of mosquito populations [108,109].
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The raw reads in opposite directions were merged using PANDAseq software , and primer sequences were trimmed out. Sequences shorter than 100 nucleotides, with any ambiguous nucleotide, or with an overlap of fewer than 20 nucleotides in paired reads were purged. The merged reads were subjected to quality control using NGSQC Toolkit , to exclude those with average Phred quality score below 30. The selected high-quality reads were proc- essed using Quantitative Insights into Microbial Ecology (QIIME V1.8) software package . Any chimeric se- quences, identified using Usearch61, were purged. The remaining reads were assigned to operational taxonomic units (OTUs) using UCLUST-based sub-sampled open- reference OTU picking protocol . A representative se- quence for each OTU was aligned with the Greengenes core set alignment using the PyNAST tool ; any se- quences that failed to align were purged. Based on align- ment of the representative OTU sequences, a phylogenetic tree was constructed using the FastTree tool . Tax- onomy was assigned to each OTU using the QIIME’s UCLUST Consensus Taxonomy Assigner against the Greengenes v13.8 reference OTUs, using the software’s de- fault parameters. Thereafter, to reduce noise, OTUs that were observed in fewer than 10% of stool specimens (n = 5) or accounted for fewer than 0.002% of reads in all the speci- mens taken together were purged out. Sample-wise obser- vation count of each OTU was tabulated as an OTU table in ‘biom’ format. The filtered OTU table was then used for determination of bacterial composition of each sample.
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There are presently no longitudinal data on the microbiota in COPD. Further, human studies have been hampered by their inability to explain the large variation in bacterial com- munities between individual samples and across subjects. Although molecular techniques have identified a novel lung microbiota in COPD, there is little information on whether alterations in the lung microbiota induce changes in the host inflammatory response. Future studies will need to address how the COPD lung microbiota affects innate and adap- tive immunity and in turn drives the formation of tertiary lymphoid follicles. Although there is strong evidence that chronic prophylactic treatment with azithromycin reduces the risk of exacerbation in COPD, it is not certain whether this effect is due to the drug’s antimicrobial or anti-inflammatory properties. Although studies of the bacterial microbiota in mice have yielded some fascinating and interesting data, their transferability to humans is not certain. At the moment, one potential role for the bacterial microbiota in the lung may be as a biomarker for worsening disease. The one generally consistent observation across the studies of the COPD micro- biome is a loss of bacterial diversity with increasing severity of disease. However, the clinical relevance of this observation
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In addition, our b-ARISA analysis showed that Ae. albopictus midgut microbiota does not differ from that of the cryptic species. MiSeq sequencing of 16S rDNA variants of 3 individuals of Ae. albopictus and 2 individ- uals of the cryptic species identified Dysgonomonas and Sphingomonadaceae as potential dominant taxa of the bacterial microbiota. The bacterial composition of Ae. albopictus midgut is strongly different from the rest of its body . Investigating midgut microbiota of seven populations from France and Vietnam, we previously discovered a similar structure across populations with the presence of the same dominant genus Dysgonomonas sp. . Individuals sampled in Vietnam also showed an enrichment of several taxa including Sphingomonada- ceae (Sphingobium, Sphingomonas, Novosphingobium). Most of these similar bacterial taxa are also found in the water and plants with which mosquitoes are in contact during immature and adult stages [38, 39]. A recent study on the Litoditis marina complex (Nematoda) described a divergent structure between the bacterial microbiota among three cryptic species . The authors suggested a link between the microbiota, intrin- sic physiological properties and trophic interactions specificities for each species. Contrary to these results, the similarity between midgut bacterial microbiota asso- ciated with the two species of the Ae. albopictus com- plex revealed here, suggests similar physiology and trophic interactions with plants and vertebrate’ hosts. However, further investigations would be needed in order to properly describe the taxonomic composition of the bacterial communities associated with the midgut of Ae. albopictus cryptic species compared to that of Ae. albopictus.
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Using combined high-throughput barcoding approaches for both bacterial and Symbiodinium com- munities, we showed that variation in Symbiodinium composition is mostly explained by thermal regime, especially minimal temperatures, whereas bacterial com- munities are much less related to temperature modifica- tions. In this context, we propose that Symbiodinium types might confer more enhanced adaptive capacities to temperature modifications than the bacterial microbiota. However, Symbiodinium clade D was known to be adapted to high temperature, and we found a negative relationship with low temperatures, suggesting low plas- ticity for this clade. Such low plasticity might limit the adaptive capabilities of a coral associated to clade D and living in highly variable thermal regime. However, a high background diversity of Symbiodinium was also ob- served, providing the potential for coral colonies to adapt or acclimatize to future environmental changes via symbiont shuffling (i.e., changes in the relative propor- tion of Symbiodinium types constituting the within host community).
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Ten samples of rain water (Table 1) were collected from water tanks from different region of Primorsko-goranska County. To test the presen- To test the presen- ce of bacterial microbiota in rainwater samples the total aerobic bacte- ria at 22 °C, 37 °C and 44 °C on Peptone yeast extract glucose agar were determined. To test the presence of indicators of fecal contamina- tions, total coliform bacteria on Les Endo agar; fecal coliform bacteria on mFC agar; intestinal enterococci on KEA agar; sulphite-reducing clo- stridia on Sulfite agar were detected by membrane filtration. For surviv- For surviv- For surviv- surviv- al studies two rainwater samples were selected according to the pres- ence of bacterial contamination and analysis were conducted in non-sterile and sterile samples. The rainwater samples were sterilized by repeated filtration through a 0.2-μm-pore-size filter.
Further analysis of the data was made on the basis of the phylogenetic classification of the sequences from each individual. The 20 most frequently occurring unique sequences in each of the 20 individuals were selected as representing the abundant microbiota for that individual. Trimmed sequences were classified at phylum to genus level using RDP II classifier and at species level using RDP II Seqmatch. A total of 210 unique sequences were taken from the two groups together for phylogenetic analyses. Labeled FASTA sequences were aligned using Geneious Pro (version 5.4.6, Drummond et al, 2011, www.geneious.com). A phylogenetic tree was built by the neighbor-joining method with genetic distance based on the Jukes-Cantor model. Sample distance matrices were constructed based on the genetic distances between individuals within groups as well as individuals in different groups and shown as heat maps. Fast Unifrac was used to calculate the P test significance and the Unifrac significance using 208 of the 210 abundant sequences. Both P test significance and Unifrac significance were calculated using 500 permutations. Unifrac was also used for assessment of the sample distance matrix.
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There are probably multiple reasons why fungal endobacteria and their hosts were largely neglected in microbiota studies so far. Reasons include the low taxonomic resolution of short-read community data or the underrepresentation of reference fungal endobacteria sequences in commonly used taxonomy databases. Here, only the combined sequencing of bacteria and fungi to- gether with the dedicated experimental design to manipulate the abundance pattern of fungal hosts and the curated fungal endo- bacteria database permitted to designate a few OTUs as ‘fungal endobacteria OTUs ’ . Our study demonstrates that microbiota and/or metagenomic datasets represent useful tools to investigate endobacterial–fungal interactions in their true ecological context. Possibly, such cultivation-independent methods can point to further endobacterial–fungal partnerships. Since fungal endobacteria are ecologically relevant for the ﬁtness of their (plant-associated) fungal hosts (Desir `o et al. 2018; Salvioli et al. 2016; Uehling et al. 2017), they may also relay some bene ﬁ ts or detriments to the host plant of the fungus (Bonfante and Desir`o 2017). Hence, mycorrhizal plants, their colonizing fungi along with their endobacteria form an entity of a multi-kingdom symbiosis. As put forward by the holobiont concept (Vandenkoornhuyse et al. 2015), the importance of multi- kingdom microbe–microbe interactions for plant performance is not only true for endobacteria and their fungal hosts but also in general between root bacteria and root fungi. For instance, root bacteria are essential to protect plants against pathogenic root fungi (Dur´an et al. 2018).
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Correlation between incidence of bacterial vaginosis and human papillomavirus: Changes in a woman's natural microbiota are directly related to human papillomavirus (HPV) infections, as women with high-risk papillomavirus infection may have a reduction in Lactobacillus spp., One of the components of the vaginal microbiota that is important peroxide producers, which may potentiate and increase the susceptibility of HIV contamination, important for maintaining cervical epithelial barrier function that inhibits HPV entry into basal keratinocytes (JUN-MO KIM & YOO JIN PARK, 2017). GB causes obstetric problems (abortion, premature birth) such as gynecological (pelvic inflammatory disease, endometritis, urinary tract infections (SILVA et al, 2019). It is one of the major cofactors related to cancer by human papillomavirus (HPV) with an incidence up to 32%. Gardnerella vaginalis bacteria may be responsible for facilitating HPV entry into epithelial cells, causing lesions in the cervicovaginal epithelium in the basal and parabasal cells, thus increasing the risk of developing cervical cancer.
Although other studies have found correlations be- tween TOC and L. pneumophila in flowing hot  and cold water systems , in this study, only the highest levels of supplemented AOC corresponded to an in- crease in L. pneumophila or other organisms of interest, while high levels even seemed to suppress Mycobacteria. Thus, there may be a threshold at which AOC control is no longer effective for specific OPs, as suggested by Wil- liams et al. . Carbon production within the building (e.g., plastics leaching carbon) and specific preferences of potential pathogens may change the community re- sponse to increased carbon. For example, some organ- isms, like Mycobacteria and P. aeruginosa, may prefer a lower range of AOC because they can out-compete others for carbon in oligotrophic stagnant environments, as has been previously observed [34, 69]. Regardless, L. pneumophila and FLA are not directly dependent on carbon available in the water, especially under warm stagnant conditions, but rather derive largely secondary influences of carbon and broader microbiota as an inter- mediary [70, 71].
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Over 17 studies from around the world have established that women’s vaginal microbiota (VMB) can be classified into one of 3 to 9 clusters or community state types (CSTs) [1–3]. The most commonly referenced typing sys- tem is that developed by Ravel et al. in 2011 . This schema describes 5 CSTs of which four CSTs were re- spectively dominated by 4 different Lactobacillus species – L. crispatus, L gasseri, L. iners and L. jensenii (Fig. 1). The fifth CST was characterized by a paucity of Lactoba- cillus spp. and an abundance of a highly diverse polymi- crobial community of facultative anaerobic BV-associated
In our previous study using a quantitative PCR and 16S rRNA gene sequencing, the bacterial count in the GF was as high as 10 8 – 10 9 /mL. 20 While many of them were supposed to be recently dead, inactivated or uncul- turable, the number was far higher than the count obtained by traditional culturing methods. Furthermore, the species richness ( α diversity) of the GF microbiota was as high as that of the faecal microbiota. These results suggested that the mass size and diversity of GF microbiota was great enough to signi ﬁ cantly affect the pathophysiology of the stomach through the metabolites and components of the bacteria. While the linkage of the alteration in the GF microbiota in the pathophysi- ology underlying FD remains to be clari ﬁ ed, the gastric mucosa might suffer from disturbance when exposed to toxic intestinal bacterial cell components like lipopoly- saccharides that stimulated leukocytes to generate pro-in ﬂ ammatory cytokines. 21 Such activation in the mucosal innate immune responses increases the mucosal permeability, which may lead to the malfunc- tion of the gastric nervous system regulating gastric motility. Bile acids are also known to exert toxic effects on gastric as well as duodenal mucosa. 22 Therefore, both of these kinds of toxic substances in the GF were suggested to be linked to the pathogenesis and patho- physiology of FD. Low-grade duodenal in ﬂ ammation has been observed and proposed as an important patho- physiological mechanism in patients with FD. 2 Recently, Vanheel et al reported that the patients with FD dis- played increased duodenal mucosal permeability that potentially resulted in mucosal in ﬂ ammation. 23 Given that lipopolysaccharides and bile acids induce an accel- eration in the mucosal permeability, the in ﬂ ammation in the duodenal region in the patients with FD might be caused by the re ﬂ uxed ﬂ uid including such potentially toxic substances. It is thought that probiotics is effective in the treatment of FD through reduction in the abun- dance of Escherichia/Shigella, a major source of toxic lipo- polysaccharides, in the upper GI tract as well as restoration of the change in the gastric microbiota. The limitations associated with the present study include the relative small number of samples and absence of the samples from the HC volunteers after LG21 yogurt treatment.
Several shoots (20 cm in length) were collected from each sampled tree, surface sterilized with 5% sodium hypochlorite (v:v), and rinsed three times in sterile water. The bark of each shoot was then removed with a sterile razor. The remaining xylem tissues were then immersed in liquid nitrogen and maintained at − 20 °C until lyophilization. Lyophilized samples were homoge- nized in a 2010 Geno/Grinder (SPEX SamplePrep, Metuchen, NJ, USA) using autoclaved metal beads. Total DNA was extracted from the ground xylem tissues using a Wizard Genomic DNA Purification Kit according to the manufacturer’s protocol (Promega, Madison, WI, USA). The quantity of each of the DNA samples was de- termined using a spectrophotometer (Nanodrop; Thermo Fisher Scientific Inc.), and the total DNA concentration was adjusted to 5.0 ng μL −1 . The fungal ITS2 region was amplified using the universal primers ITS3/KYO2 and ITS4 to amplify the ITS2 region of the ribosomal DNA . The bacterial 16S region was amplified using the protocol described by Lundberg et al. , including the use of a pair of peptide-nucleic-acids (PNA) that were in- corporated into the PCR amplification in order to reduce the generation of non-target chloroplast and mitochon- drial amplicons. The universal 16S primer pair 515F and 806R was used to generate bacterial-derived 16S ampli- cons . All primers were modified to include Illumina adaptors (www.illumina.com). PCR reactions were con- ducted in a total volume of 25 μL containing 12.5 μL of KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Wil- mington, MA, USA), 1.0 μL of each primer (10 μM), 2.5 μL of DNA template, and 8.0 μL nuclease-free water. The reactions were incubated in a T100 thermal cycler (Bio-Rad) for 3 min at 98 °C followed by 30 cycles of 30 s at 95 °C, 30 s at 50 °C, and 30 s at 72 °C. All reactions ended with a final extension of 1 min at 72 °C. Nuclease- free water (QIAGEN, Valencia, CA, USA) replaced tem- plate DNA in negative controls. All amplicons and amplification mixtures including negative controls were sequenced on a MiSeq platform using V2 chemistry (Illumina, San Diego, CA, USA).
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Fecal transplant refers to any method of delivery of healthy human stool to the colon of a recipient. This therapy is now gaining standard-of-care designation in the United States, Australia, and many parts of Europe for treating resistant Clostridium difficile infection). This literature review describes fecal transplant protocols. It highlights the variety of techniques used to screen stool donors; prepare and deliver treatment; and how, despite these variations, safety and efficacy remain high. It highlights the various ways to best mitigate safety while also recommending the direction in which clinical and research communities can move to continue to provide access to fecal microbiota transplant in a cost-effective manner.
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In addition to being a passage for sperm, menstruum, and the baby, the human vagina and its microbiota can influence conception, pregnancy, the mode and timing of delivery, and the risk of acquiring sexually transmitted infections. The physiological status of the vaginal milieu is important for the wellbeing of the host as well as for successful reproduction. High estrogen states, as seen during puberty and pregnancy, promote the preservation of a homeostatic (eubiotic) vaginal microenvironment by stimulating the maturation and proliferation of vaginal epithelial cells and the accumulation of glycogen. A glycogen-rich vaginal milieu is a haven for the proliferation of Lactobacilli facilitated by the production of lactic acid and decreased pH. Lactobacilli and their antimicrobial and anti-inflammatory products along with components of the epithelial mucosal barrier provide an effective first line defense against invading pathogens including bacterial vaginosis, aerobic vaginitis-associated bacteria, viruses, fungi and protozoa. An optimal host-microbial interaction is required for the maintenance of eubiosis and vaginal health. This review explores the composition, function and adaptive mechanisms of the vaginal microbiome in health and those disease states in which there is a breach in the host-microbial relationship. The potential impact of vaginal dysbiosis on reproduction is also outlined.
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Using 16S rRNA gene absolute abundance as a surrogate of taxon absolute abundance in this study was key to elucidating the associations between Nugent score and penile microbiota, likely because taxon absolute abundance is the most relevant metric for examining ecological interactions (40). However, to better evalu- ate our surrogate metric’s clinical interpretation and to more fully assess the influence of penile bacteria on female partner vaginal microbiota and vice versa, longitudinal partner studies are needed to assess treatments that eradicate BV-associated bacteria from men and the temporal effects of sexual intercourse on genital mi- crobiota. It will also be important to determine if our findings could be generalized to non-Ugandan populations. Previous stud- ies suggest that antimicrobial resistance and poor drug penetra- tion can challenge decolonization efforts (41–45). However, study design limitations—including, suboptimal treatment regimen, insufficient randomization methods, limited power, and un- known adherence—may have contributed to previous failed at- tempts to decrease BV by decolonizing male sexual partners (46). If BV is redefined as a sexually transmitted condition, it has the potential to expand the infectious disease framework from trans- mission of single pathogens to encompass transmission of bacte- rial communities. This could affect clinical care of BV and justify new preventative and treatment strategies, such as prebiotic, pro- biotics, or narrow-spectrum antimicrobials to modify the penile microbiota or microenvironments aimed at reducing male car- riage, which may ameliorate the persistence and recurrence of BV.