Microbiology
Abstract
To radically diminish TB incidence and mortality by 2035, as set out by the WHO End TB Strategy, there is a desperate need for improved TB therapies and a more effective vaccine against the deadly pathogen Mycobacterium tuberculosis (Mtb). Aerosol vaccination with the MtbΔsigH mutant protects two different species of NHPs against lethal TB challenge by invoking vastly superior T and B cell responses in the lungs through superior antigen-presentation and interferon-conditioning. Since the Geneva consensus on essential steps towards the development of live mycobacterial vaccines recommends that live TB vaccines must incorporate at least two independent gene knock outs, we have now generated several rationally designed, double (DKO)- and triple (TKO) knock-out mutants in Mtb, each containing the ΔsigH deletion. Here, we report preclinical studies in the rhesus macaque model of aerosol infection and SIV/HIV co-infection, aimed at assessing the safety of these MtbΔsigH - based DKOs and TKOs. We found that most of these mutant strains are attenuated in both immunocompetent and SIV-co-infected macaques and combinatorial infection with these generated strong cellular immune responses in the lung, akin to MtbΔsigH. Aerosol infection with these KO strains elicited inducible Bronchus Associated Lymphoid Tissue (iBALT), which is a correlate of protection from TB.
Authors
Garima Arora, Caden W. Munson, Mushtaq Ahmed, Vinay Shivanna, Annu Devi, Venkata S.R. Devireddy, Basil Antony, Shannan Hall-Ursone, Olga D. Gonzalez, Edward Dick Jr., Chinnaswamy Jagannath, Xavier Alvarez, Smriti Mehra, Shabaana A. Khader, Dhiraj K. Singh, Deepak Kaushal
Abstract
Multidrug-resistant (MDR) bacterial pneumonias pose a critical threat to global public health. The opportunistic Gram-negative pathogen Pseudomonas aeruginosa is a leading cause of nosocomial-associated pneumonia, and an effective vaccine could protect vulnerable populations, including the elderly, immunocompromised, and those with chronic respiratory diseases. Highly heterogeneous outer membrane vesicles (OMVs), shed from Gram-negative bacteria, are studded with immunogenic lipids, proteins, and virulence factors. To overcome limitations in OMV stability and consistency, we described a believed to be novel vaccine platform that combines immunogenic OMVs with precision nanotechnology—creating a bacterial cellular nanoparticle vaccine candidate (CNP), termed Pa-STING-CNP, which incorporates an adjuvanted core that activates the STING (stimulator of interferon genes) pathway. In this design, OMVs are coated onto the surface of self-adjuvanted STING nanocores. Pa-STING CNP vaccination induced substantial antigen presenting cell recruitment and activation in draining lymph nodes, robust anti-Pseudomonas antibody responses, and provided protection against lethal challenge with the hypervirulent clinical P. aeruginosa isolate PA14. Antibody responses mediated this protection and provided passive immunity against the heterologous P. aeruginosa strain PA01. These findings provided evidence that nanotechnology can be used to create a highly efficacious vaccine platform against high priority MDR pathogens such as P. aeruginosa.
Authors
Elisabet Bjånes, Nishta Krishnan, Truman Koh, Anh T.P. Ngo, Jason Cole, Joshua Olson, Ingrid Cornax, Chih-Ho Chen, Natalie Chavarria, Samira Dahesh, Shawn M. Hannah, Alexandra Stream, Jiaqi Amber Zhang, Hervé Besançon, Daniel Sun, Siri Yendluri, Sydney Morrill, Jiarong Zhou, Animesh Mohapatra, Ronnie H. Fang, Victor Nizet
Citation Information: JCI Insight. 2025;10(14):e188993. https://doi.org/10.1172/jci.insight.188993.
Abstract
Background Ready-to-use supplemental foods (RUSF) are energy-dense meals used to treat moderate and severe acute childhood malnutrition. Weight recovery with RUSF is heterogeneous, therefore we investigated whether environmental enteric dysfunction (EED), systemic inflammation, and gut microbiota predict RUSF response.Methods We followed nutritional status and RUSF outcomes in a rural birth cohort of 416 Pakistani infants. Acha Mum, a chickpea-based RUSF, was administered daily for 8 weeks to children who developed wasting (weight-for-length Z-score <–2).Results Of 187 treated with RUSF, 112 showed no immediate improvement in weight-for-age. Machine learning identified nine biomarkers that collectively predicted RUSF response with 73% accuracy. Gut microbiome composition before and after supplementation predicted response with 93% and 98% accuracy, respectively. Responders showed microbiome restructuring, with increased growth-associated taxa and reduced Gammaproteobacteria relative to nonresponders. A subset of extreme nonresponders—whose microbiome profiles resembled those of responders—displayed markedly abnormal biomarkers of inflammation, suggesting adverse host factors constrain gut microbiota benefits for RUSF efficacy.Conclusion EED, systemic inflammation, and gut microbiota predict acute nutritional responses to Acha Mum, setting the stage for precision use of RUSF and adjunctive therapies in addressing the global burden of childhood malnutrition in low- and middle-income countries.
Authors
Zehra Jamil, Gabriel F. Hanson, Junaid Iqbal, G. Brett Moreau, Najeeha Talat Iqbal, Sheraz Ahmed, Aneeta Hotwani, Furqan Kabir, Fayaz Umrani, Kamran Sadiq, Kumail Ahmed, Indika Mallawaarachchi, Jennie Z. Ma, Fatima Aziz, S. Asad Ali, Sean R. Moore
Citation Information: JCI Insight. 2025;10(13):e183123. https://doi.org/10.1172/jci.insight.183123.
Abstract
Bacteriophages, viruses that parasitize bacteria, are abundant in the human microbiome and may influence human health, in part, through their interactions with bacterial hosts. Whether endogenous bacteriophages or their products are vertically transmitted from mother to fetus during human pregnancy is not known. Here, we searched for bacteriophage sequences from five bacteriophage databases (474,031 total sequences) in cell-free DNA (cfDNA) of paired maternal and umbilical cord blood samples from two independent cohorts. First, we sequenced cfDNA from 10 pairs of maternal and cord blood samples, including four pairs affected by preeclampsia. We validated our findings in a previously published dataset of 62 paired maternal and cord blood samples, including 43 pairs from preterm or chorioamnionitis-affected deliveries. We identified 94 and 596 bacteriophage sequences in maternal and cord blood cfDNA samples from the first and second cohort, respectively. We identified 58 phage sequences across maternal-infant dyads and 581 phage sequences that were unique to a single sample. We did not identify any phage sequences consistently associated with preeclampsia, preterm, or chorioamnionitis-affected samples. This study demonstrated the presence of bacteriophage DNA in human cord blood at birth, providing evidence that the human fetus is exposed to bacteriophage DNA in utero.
Authors
Jennifer A. Sequoia, Naomi L. Haddock, Paw Mar Gay, Layla J. Barkal, Purnima Narasimhan, Nadine Martinez, Virginia D. Winn, Paul L. Bollyky
Citation Information: JCI Insight. 2025. https://doi.org/10.1172/jci.insight.187683.
Abstract
Bariatric surgery is associated with improved breast cancer (BC) outcomes, including greater immunotherapy effectiveness in a pre-clinical BC model. A potential mechanism of bariatric surgery-associated protection is the gut microbiota. Here, we demonstrate the dependency of improved immunotherapy response on the post-bariatric surgery gut microbiome via fecal microbial transplant (FMT). Response to αPD-1 immunotherapy was significantly improved following FMT from formerly obese bariatric surgery-treated mice. When stool from post-bariatric surgery patients was transplanted into recipient mice and compared to the patients’ pre-surgery transplants, post-surgery microbes significantly reduced tumor burden and doubled immunotherapy effectiveness. Microbes impact tumor burden through microbially derived metabolites, including branched chain amino acids (BCAA). Circulating BCAAs correlated significantly with natural killer T (NKT) cell content in the tumor microenvironment in donor mice after bariatric surgery and FMT recipients of donor cecal content after bariatric surgery compared to obese controls. BCAA supplementation replicated improved αPD-1 effectiveness in two BC models, supporting the role of BCAAs in increased immunotherapy effectiveness after bariatric surgery. Ex vivo exposure increased primary NKT cell expression of anti-tumor cytokines, demonstrating direct activation of NKT cells by BCAAs. Together, findings suggest that reinvigorating anti-tumor immunity may depend upon bariatric surgery-associated microbially derived metabolites, namely BCAAs.
Authors
Margaret S. Bohm, Sydney C. Joseph, Laura M. Sipe, Minjeong Kim, Cameron T. Leathem, Tahliyah S. Mims, Nathaniel B. Willis, Ubaid A. Tanveer, Joel H. Elasy, Emily W. Grey, Madeline E. Pye, Zeid T. Mustafa, Barbara Anne Harper, Logan G. McGrath, Deidre Daria, Brenda Landvoigt Schmitt, Jelissa A. Myers, Patricia Pantoja Newman, Brandt D. Pence, Marie Van der Merwe, Matthew J. Davis, Joseph F. Pierre, Liza Makowski
Citation Information: JCI Insight. 2025;10(8):e186505. https://doi.org/10.1172/jci.insight.186505.
Abstract
Transplant recipients require lifelong, multimodal immunosuppression to prevent rejection by reducing alloreactive immunity. Rapamycin is known to modulate adaptive and innate immunity, but its full mechanism remains incompletely understood. We investigated the understudied effects of rapamycin on lymph node (LN) architecture, leukocyte trafficking, and gut microbiome and metabolism after 3 (early), 7 (intermediate), and 30 (late) days of rapamycin treatment. Rapamycin significantly reduced CD4+ T cells, CD8+ T cells, and Tregs in peripheral LNs, mesenteric LNs, and spleen. Rapamycin induced early proinflammation transition to protolerogenic status by modulating the LN laminin α4/α5 expression ratios (La4/La5) through LN stromal cells, laminin α5 expression, and adjustment of Treg numbers and distribution. Additionally, rapamycin shifted the Bacteroides/Firmicutes ratio and increased amino acid bioavailability in the gut lumen. These effects were evident by 7 days and became most pronounced by 30 days in naive mice, with changes as early as 3 days in allogeneic splenocyte-stimulated mice. These findings reveal what we believe to be a novel mechanism of rapamycin action through time-dependent modulation of LN architecture and gut microbiome, which orchestrates changes in immune cell trafficking, providing a framework for understanding and optimizing immunosuppressive therapies.
Authors
Long Wu, Allison Kensiski, Samuel J. Gavzy, Hnin Wai Lwin, Yang Song, Michael T. France, Ram Lakhan, Dejun Kong, Lushen Li, Vikas Saxena, Wenji Piao, Marina W. Shirkey, Valeria R. Mas, Bing Ma, Jonathan S. Bromberg
Citation Information: JCI Insight. 2025. https://doi.org/10.1172/jci.insight.188146.
Abstract
Pf bacteriophages, lysogenic viruses that infect Pseudomonas aeruginosa (Pa), are implicated in the pathogenesis of chronic Pa infections; phage-infected (Pf+) strains are known to predominate in people with cystic fibrosis (pwCF) who are older and have more severe disease. However, the transmission patterns of Pf underlying the progressive dominance of Pf+ strains are unclear. In particular, it is unknown whether phage transmission commonly occurs horizontally between bacteria via viral particles within the airway or if Pf+ bacteria are mostly acquired via de novo Pseudomonas infections. Here, we studied Pa genomic sequences from 3 patient cohorts totaling 662 clinical isolates from 105 pwCF. We identified Pf+ isolates and analyzed transmission patterns of Pf within patients between genetically similar groups of bacteria called “clone types”. We found that Pf was predominantly passed down vertically within Pa clone types and rarely via horizontal transfer between clone types within the airway. Conversely, we found extensive evidence of Pa de novo infection by a new, genetically distinct Pf+ Pa. Finally, we observed that clinical isolates showed reduced activity of the type IV pilus and reduced susceptibility to Pf in vitro. These results cast new light on the transmission of virulence-associated phages in the clinical setting.
Authors
Julie D. Pourtois, Naomi L. Haddock, Aditi Gupta, Arya Khosravi, Hunter A. Martinez, Amelia K. Schmidt, Prema S. Prakash, Ronit Jain, Piper Fleming, Tony H. Chang, Carlos Milla, Patrick R. Secor, Giulio A. De Leo, Paul L. Bollyky, Elizabeth B. Burgener
Citation Information: JCI Insight. 2025. https://doi.org/10.1172/jci.insight.176839.
Abstract
The standard-of-care treatment of locally advanced cervical cancer includes pelvic radiation therapy with concurrent cisplatin-based chemotherapy and is associated with a 30-50% failure rate. New prognostic and therapeutic targets are needed to improve clinical outcomes. The vaginal microbiome has been linked to the pathogenesis of cervical cancer, but little is known about the vaginal microbiome in locally advanced cervical cancer as it relates to chemoradiation. In this pilot study we utilized 16S rRNA gene community profiling to characterize the vaginal microbiomes of 26 postmenopausal women with locally advanced cervical cancer receiving chemoradiation. Our analysis revealed diverse anaerobe-dominated communities whose taxonomic composition, diversity or bacterial abundance did not change with treatment. We hypothesized that characteristics of the microbiome might correlate with treatment response. Pretreatment microbial diversity and bacterial abundance were not associated with disease recurrence. We observed a greater relative abundance of Fusobacterium in patients that later had cancer recurrence, suggesting that Fusobacterium could play a role in modifying treatment response. Taken together, this hypothesis generating pilot study provides insight into the composition and dynamics of the vaginal microbiome, offering proof-of-concept for future study of the microbiome and its relationship with treatment outcomes in locally advanced cervical cancer.
Authors
Brett A. Tortelli, Jessika Contreras, Stephanie Markovina, Li Ding, Kristine M. Wylie, Julie K. Schwarz
Citation Information: JCI Insight. 2025. https://doi.org/10.1172/jci.insight.186003.
Abstract
Chagas disease is a neglected tropical disease caused by Trypanosoma cruzi with clinical presentations ranging from asymptomatic to cardiac and/or gastrointestinal complications. The mechanisms of pathogenesis are still poorly understood, but T. cruzi strain diversity may be associated with disease progression. Therefore, we evaluated the transcriptomic response of PBMCs from macaques with natural chronic infections and tested for heterogeneity in their gene signatures. Remarkably, transcriptomic response to T. cruzi infection matched parasite strain profiles, indicating that parasite diversity is a key determinant of host response. While differences in adaptive immune responses were identified, more striking alterations of innate immune processes were detected. Thus, initial innate response to T. cruzi infection may be conditioned by parasite strain diversity, resulting in different profiles of trained immunity modulating subsequent adaptive responses, allowing parasite control or its persistence during the chronic phase. These results call for further characterization of the cross-talk between innate and adaptive immunity according to parasite diversity, and how altered trained immunity contributes to pathogenesis, as this may lead to better treatments and vaccines.
Authors
Hans Desale, Weihong Tu, Kelly Goff, Preston A. Marx, Claudia Herrera, Eric Dumonteil
Citation Information: JCI Insight. 2025. https://doi.org/10.1172/jci.insight.186649.
Abstract
Authors
Jing Zeng, Derrick Zhao, Grayson Way, Andrew Fagan, Michael Fuchs, Puneet Puri, Brian C. Davis, Xuan Wang, Emily C. Gurley, Phillip B. Hylemon, Jian-Gao Fan, Masoumeh Sikaroodi, Patrick M. Gillevet, Huiping Zhou, Jasmohan S. Bajaj
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