The research team, led by scientists at the Ocean University of China working with collaborators at the BYHEALTH Institute of Nutrition and Health and other Chinese institutions, set out to investigate whether chronic, low-level antibiotic exposure could trigger adaptive responses in this non-spore-forming bacterium. Unlike spore-forming species such as Bacillus, which can build tough, desiccated spores to ride out hostile conditions, Lactobacillus species have long been considered relatively fragile outside their comfortable niches. Bacterial dormancy offers an alternative strategy: a metabolically suppressed but fully reversible state that allows non-spore-forming bacteria to withstand adverse conditions without constructing specialized survival structures. The researchers exposed the sp1.1 strain of L. delbrueckii subsp. bulgaricus to concentrations of rifampicin that stressed but did not kill the cells, then tracked what happened to their physiology, their stress resistance, and their behavior in living animals.

The results were striking. Rifampicin-treated cells entered a state the authors characterize as dormancy, marked by sharply reduced ATP levels, the cellular energy currency, and impaired cell division. The bacteria essentially throttled themselves down, halting growth and conserving resources. Crucially, the state was reversible: when the antibiotic stress was removed, colonies recovered and normal growth resumed. This reversibility distinguishes dormancy from death and from irreversible injury, and it suggests a programmed, controlled response rather than simple damage. In the food industry, where starter cultures routinely face freezing, drying, acidification, and thermal processing steps that whittle down viable cell counts, a reversible dormant state that confers cross-tolerance to multiple stressors at once would be an enormously valuable property.

And cross-tolerance is exactly what the team observed. Dormant cells tolerated acid, alkali, and heat stress significantly better than untreated controls, meaning a single trigger, sublethal rifampicin exposure, produced broad-spectrum resistance rather than protection against just one threat. The functional consequences extended beyond the laboratory bench. When the researchers administered the treated bacteria to mice, the dormant cells persisted longer in the intestinal tract than normal cells, a property known as prolonged intestinal retention. They also exerted a greater impact on the structure of the gut microbial community, indicating that the dormant state changes not just survival but ecological behavior once the bacteria reach the gut. For probiotic formulations, where the central challenge is delivering enough live cells through gastric acid and bile to produce a benefit, these findings point to a potentially powerful new lever.

The mechanism behind this transformation turned out to be one of the most intriguing aspects of the study. When the researchers disrupted the protein aggregates that formed in the dormant cells, either by adjusting pH or by treating the cells with 1,6-hexanediol, a chemical that dissolves certain types of protein condensates, the enhanced tolerance vanished entirely. That causal experiment established that the aggregates are not a byproduct of dormancy but its functional engine. Rifampicin, which targets RNA polymerase and inhibits transcription, triggered a metabolic shift toward transcriptional and translational inhibition, and as protein synthesis slowed, proteins began to clump together into aggregates within the cells. What could have been cellular garbage, however, turned out to be something far more purposeful.

Proteomic analysis of the aggregates revealed a striking selectivity. Rather than capturing random cellular proteins, the aggregates were enriched for proteins involved in translation, RNA metabolism, and DNA repair, precisely the functions a cell would need to restart growth once conditions improve. The authors propose a model in which these aggregates function as molecular safe houses, sequestering and protecting key proteins from degradation or damage during the dormant period. By concentrating translation and DNA repair machinery in one protected location, the aggregates may locally enhance the efficiency of those processes when the cell revives, while also serving as a protein reservoir that allows rapid recovery of growth. In this view, the aggregate is less like a junk pile and more like a sealed emergency kit, packed with the tools needed for reconstruction.

Two intrinsically disordered proteins, identified in the study as Gene1622 and Gene1909, emerged as likely architects of this process. Disordered proteins lack a fixed three-dimensional structure and are known drivers of biomolecular condensate formation in many organisms. In the rifampicin-treated bacteria, both proteins were upregulated in whole-cell measurements and were enriched within the aggregates, suggesting they help nucleate or organize the condensates. The involvement of disordered proteins links this bacterial phenomenon to a broader and rapidly growing body of research on biomolecular condensates, membrane-less compartments that cells across all domains of life use to organize their biochemistry. That a food bacterium uses condensate biology to survive antibiotic stress adds a new ecological dimension to what has largely been studied in model organisms and human cells.

The study also uncovered hidden diversity within the bacterial population. Using single-cell RNA sequencing, the researchers identified a subpopulation of cells that sustained expression of alaS and gatA, genes involved in translation, even while global protein synthesis was being suppressed. These genes were downregulated in bulk RNA sequencing, which averages signals across the whole population, but single-cell analysis revealed that a distinct cluster of cells kept them active. This population heterogeneity means that not all cells respond identically to antibiotic stress; some appear to hedge their bets, maintaining critical functions while their neighbors go fully dormant. Such bet-hedging strategies are well known in microbial ecology, and this study demonstrates them at single-cell resolution in a commercially important probiotic, showing how a population can prepare for recovery even while most of its members are shut down.

The implications cut in two directions. On the constructive side, the findings provide a theoretical basis for engineering more robust starter cultures and probiotics. If manufacturers can deliberately induce and control this reversible dormant state, perhaps through stress conditioning rather than antibiotic exposure, they could produce cultures that survive processing better, retain viability longer on the shelf, and persist more effectively in the gut. The authors note that the work was supported by the National Natural Science Foundation of China and the BYHEALTH Nutrition and Health Research Foundation, reflecting industry interest in exactly these applications. On the cautionary side, the study raises ecological questions about stress-induced adaptation in the food chain. Antibiotic residues at sublethal levels are a known feature of some food production environments, and this research shows that such exposure can make food bacteria hardier and more persistent in the gut, where they exert stronger effects on microbial community structure. Whether that enhanced persistence is beneficial or disruptive to gut microbial homeostasis remains an open question, and one the authors flag explicitly. As the boundaries between food microbiology, antibiotic stewardship, and gut ecology continue to blur, this study suggests that the microbes in our yogurt may be far more adaptable, and far more responsive to their chemical environment, than anyone assumed.

Subject of Research: Sublethal antibiotic-induced dormancy and protein aggregation in Lactobacillus delbrueckii subsp. bulgaricus

Article Title: Sublethal rifampicin enhances the tolerance of Lactobacillus delbrueckii subsp. bulgaricus to food processing and intestinal retention through protein aggregation

Article References: Liu, L., Li, Z., Di, C., Ma, C., Huang, Y., Hao, X., Fu, Z., Yi, H., Zhang, Z., Li, P., Li, L., Ze, X., He, R., Zhang, L., & Gong, P. (2026). Sublethal rifampicin enhances the tolerance of Lactobacillus delbrueckii subsp. bulgaricus to food processing and intestinal retention through protein aggregation. Microbiome. https://doi.org/10.1186/s40168-026-02517-3

Image Credits: AI Generated

DOI: 10.1186/s40168-026-02517-3

Keywords: Lactobacillus delbrueckii subsp. bulgaricus, rifampicin, bacterial dormancy, protein aggregates, probiotics, starter cultures, gut microbiome, stress tolerance, single-cell RNA sequencing, intrinsically disordered proteins, food fermentation, intestinal retention

The assay under scrutiny is Deeplex Myc-TB, a targeted next-generation sequencing test developed to detect mutations in the tuberculosis genome that are associated with resistance to a broad range of first- and second-line anti-TB drugs. Unlike conventional rapid molecular tests, which typically interrogate only a handful of genetic regions, targeted sequencing approaches can survey dozens of genes and intergenic regions in a single run. This breadth matters enormously in clinical practice, because treatment decisions for multidrug-resistant and extensively drug-resistant tuberculosis depend on knowing, quickly and reliably, which drugs are likely to fail and which are likely to work.

To evaluate the assay, the researchers turned to an unusual but powerful resource: isolates distributed through the World Health Organization global Tuberculosis Drug-Susceptibility Testing Proficiency Testing Program, organized and administered by the TB Supranational Reference Laboratory in Antwerp, Belgium. A total of 41 isolates were included in the study. These samples are particularly valuable for verification work because they have been exhaustively characterized by reference laboratories using multiple independent methods. In this study, phenotypic drug susceptibility testing performed on Löwenstein-Jensen medium and in mycobacteria growth indicator tube culture, together with whole-genome sequencing, served as the reference standards against which the Deeplex assay was judged.

The analytical workflow was straightforward in concept. Remnant DNA extracted from the proficiency testing isolates was subjected to targeted next-generation sequencing using the Deeplex Myc-TB assay. The resulting sequence data were interpreted using the manufacturer’s Deeplex web application, and, in parallel, with TBProfiler, an open-source tool for predicting drug resistance from mycobacterial sequence data, applying a composite interpretation rule. Concordance, sensitivity, and specificity were then calculated for each drug class, providing a detailed picture of where the assay excels and where it falls short.

The headline result is striking: the Deeplex Myc-TB assay achieved 100 percent specificity across all drug targets examined. In diagnostic terms, this means that whenever the assay reported a resistance mutation, the isolate genuinely carried a mutation associated with resistance. False positives, which can lead clinicians to withhold effective drugs unnecessarily, were entirely absent from the dataset. For several drugs, the assay’s sensitivity was equally impressive. It correctly identified resistance in every tested isolate for rifampicin, detecting 17 of 17 resistant strains; for pyrazinamide, 7 of 7; for fluoroquinolones, 13 of 13; and for linezolid, 6 of 6. For isoniazid, sensitivity was 94.1 percent, with 16 of 17 resistant isolates correctly flagged.

The single isoniazid miss is instructive rather than alarming. The one false-susceptible result traced back to a specific insertion mutation in the katG gene, designated katG c.45_46insA, which fell outside the region targeted by the assay. This illustrates a fundamental property of targeted sequencing: its performance is bounded by the mutations it is designed to detect. When a resistance-conferring variant lies outside the panel’s target regions, even a technically flawless assay will report susceptibility. The finding underscores why laboratories adopting such assays must understand the local epidemiology of resistance mutations in the strains they encounter.

Performance was more mixed for the newer and repurposed drugs that have become central to modern regimens for drug-resistant tuberculosis. For clofazimine, the assay detected resistance in 4 of 5 phenotypically resistant isolates, a sensitivity of 80 percent. For bedaquiline, sensitivity dropped to 44.4 percent, with only 4 of 9 resistant strains correctly identified. In five cases, isolates that were resistant by phenotypic testing carried no resistance variants detected by the assay. The authors traced much of this gap to the biology of resistance to these drugs. Mutations in the mmpR5 gene, also known as Rv0678, a major regulator of efflux pump expression, were largely detected by the assay, but resistance mediated through the atpE gene was not identified, because that gene is not adequately covered by the assay’s target panel.

Overall concordance between the Deeplex assay and the reference standards ranged from 87.5 percent for bedaquiline to a perfect 100 percent for rifampicin, pyrazinamide, fluoroquinolones, and linezolid. Notably, the assay consistently detected several recurrent mutations associated with resistance to the different drugs, reinforcing the idea that for the common, well-established resistance mechanisms, targeted sequencing performs at or near the level of whole-genome sequencing while being faster and cheaper to deploy in routine laboratory settings. For a disease where every week of delayed or inappropriate treatment increases the risk of transmission, disease progression, and death, that speed advantage carries real clinical weight.

The implications of this verification study extend well beyond one laboratory in Uganda. Proficiency testing panels offer a rare opportunity to benchmark a diagnostic assay against isolates whose resistance profiles are known with high confidence, free from the uncertainties that complicate evaluations using routine clinical samples. By demonstrating near-perfect specificity and strong sensitivity for the cornerstone drugs of tuberculosis therapy, the study provides laboratories considering adoption of targeted next-generation sequencing with concrete, independently grounded performance data. At the same time, the documented gaps for bedaquiline and clofazimine serve as a caution against treating any single assay as a complete solution. The authors emphasize that understanding local resistance mutation patterns is essential when implementing sequencing-based resistance detection, because an assay that misses the mutations circulating in a given region will systematically underreport resistance there.

The broader context makes these findings timely. Drug-resistant tuberculosis kills thousands of people each year, and the introduction of bedaquiline, linezolid, and other newer agents has transformed outcomes for patients with resistant disease, but only when those drugs are deployed appropriately. Molecular diagnostics that can rapidly and accurately profile resistance across the full range of current and repurposed drugs are a critical link in that chain. This study shows that targeted sequencing platforms have matured to the point where they can match reference standards for the most important drugs, while also mapping precisely where the remaining blind spots lie. For laboratory directors, national tuberculosis programs, and diagnostic developers alike, the message is twofold: the technology is ready for prime time in the core of TB drug resistance testing, but careful attention to target coverage, and to the mutation landscape of the populations being served, remains indispensable.

Subject of Research: Analytical performance verification of a targeted next-generation sequencing assay for detecting drug-resistant Mycobacterium tuberculosis

Article Title: Analytical performance verification of the Deeplex Myc-TB assay using well-characterized Mycobacterium tuberculosis proficiency testing isolates

Article References: Kabahita, J. M., Lunkuse, J. M., Batte, D. N., Nakato, H. S., Namutebi, J., Kabugo, J., Adam, I., Kanyerezi, S., Makoha, C., Nsubuga, M. L., Oundo, H. R., Wenka, G. T., Sseruyange, J., Murungi, M., Kasule, G. W., Lutaaya, P., Kyokushaba, J., Byabajungu, H., Ademun, P., … Joloba, M. L. (2026). Analytical performance verification of the Deeplex Myc-TB assay using well-characterized Mycobacterium tuberculosis proficiency testing isolates. BMC Genomics. https://doi.org/10.1186/s12864-026-13336-z

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13336-z

Keywords: tuberculosis, drug resistance, Deeplex Myc-TB, targeted next-generation sequencing, whole-genome sequencing, diagnostics, bedaquiline, clofazimine, isoniazid, rifampicin, proficiency testing, Uganda

The first patient was a four-year-old neutered male Savannah cat from Inverness, Scotland, who was presented to his general practice veterinarian with an intermittent cough and mild weight loss lasting three weeks. The cat was strictly indoor-only and had been fed a commercially available raw meat-based diet containing poultry and supplemental beef offal. Initial treatment with the anti-inflammatory drug meloxicam produced no response, and over the following two weeks the cough became more persistent while the cat grew increasingly lethargic with a reduced appetite.

Thoracic radiographs revealed a marked broncho-interstitial lung pattern, and a blind bronchoalveolar lavage performed under anaesthesia showed moderate neutrophilic inflammation but was negative on routine bacterial culture. An empirical course of the antibiotic marbofloxacin also failed to help. By the time the cat was referred to a specialist institution, he had lost 30 percent of his body weight. A computed tomography scan showed severe, diffuse nodular to confluent soft tissue lesions affecting all lung lobes, together with enlarged mediastinal lymph nodes. Fine-needle aspirates of consolidated lung tissue revealed severe pyogranulomatous inflammation, and Ziehl-Neelsen staining identified small numbers of acid-fast bacilli with the slender, curved morphology typical of mycobacteria. Culture subsequently confirmed Mycobacterium caprae.

Treatment began with a triple antibiotic protocol comprising pradofloxacin at 5 mg/kg, rifampicin at 10 mg/kg and azithromycin at 15 mg/kg, each given orally once daily in liquid formulations. An oesophagostomy tube was placed to help the owners administer the prolonged medication with minimal stress. The cat was hospitalised in isolation for eight days with strict infection control precautions, including personal protective equipment for staff. Public health officials were notified once the diagnosis was confirmed, but no further testing of in-contact people was deemed necessary. Clinically, the cat improved rapidly, gaining weight within a month and coughing far less frequently. Although repeat radiographs at three-monthly intervals showed only mild improvement, treatment was stopped after eleven months when lung changes had remained static for more than two months. The cat remains clinically normal a year after therapy ended.

The second patient was a three-year-old neutered female British Shorthair from Hampshire, England, who was fed the same raw meat-based diet product and presented with a one-month history of cough, weight loss and fever. Radiographs revealed a cavitating mass in the caudal left lung field, a large nodule in the left cranial lung and multifocal areas of dense consolidation throughout the remaining lung fields. Cytology of a bronchoalveolar lavage sample showed marked neutrophilic and macrophagic inflammation with epithelioid macrophages containing non-staining ghost bacilli, and Ziehl-Neelsen staining again revealed intracellular acid-fast organisms. Polymerase chain reaction testing at a mycobacterial reference laboratory detected DNA of the Mycobacterium tuberculosis complex, and sequencing confirmed M. caprae.

The same triple antibiotic regimen was prescribed, again using liquid formulations to support long-term daily compliance. The cat improved rapidly, gaining weight within a month, with coughing notably reduced by four months of therapy. Radiographs after five months showed significant improvement without complete normalisation, and after a further three months the findings were unchanged. Given the patient was clinically well and had completed nine months of treatment, therapy was discontinued. She remains clinically normal ten months after cessation.

The clinical significance of these cases extends beyond the rarity of the pathogen. In the United Kingdom, feline infections with the M. tuberculosis complex are usually caused by Mycobacterium bovis or Mycobacterium microti, and M. caprae has only recently been identified in domestic cats, previously documented in detail in a single post-mortem case. The treatment protocol used in both cats was adapted from human tuberculosis guidelines and consists of rifampicin, a fluoroquinolone and a macrolide continued for at least three months and for two months beyond resolution of clinical signs. Earlier retrospective work found that only 42 percent of treated cats achieved complete remission, often despite inappropriate therapy, whereas the updated multidrug approach has produced remission rates of approximately 80 percent.

Notably, neither cat achieved radiographic resolution despite extended therapy, yet both remained free of relapse. The authors draw an analogy with post-tuberculosis lung disease in humans, an increasingly recognised spectrum of structural and functional pulmonary abnormalities that persists after successful anti-mycobacterial therapy in 18 to 80 percent of treated patients. They suggest that stable radiographic changes could serve as a reasonable therapeutic endpoint in feline mycobacterial infections where initial lung damage is too severe to be expected to normalise.

The report also underscores the practical demands of treatment. Both cats required prolonged daily multidrug therapy with frequent follow-up visits, demanding substantial financial and emotional investment from their owners alongside excellent patient compliance. The authors caution that where such commitment is not feasible, euthanasia should be considered for severely affected animals, both for welfare reasons and to reduce the risk of antimicrobial resistance developing from inconsistent dosing. They further note that empirical treatment choices early in the diagnostic process, such as anti-inflammatory drugs, can complicate or worsen the clinical course and should be weighed carefully with owners.

Zoonotic considerations shaped the management of both cases. Transmission of M. bovis from cats to humans has been documented previously, although the risk is considered very low, and M. caprae transmission to humans has only been identified in proximity to infected goats, its reservoir host, never from cats. Because no in-contact humans had risk factors for zoonotic transmission, treatment of both cats was judged reasonable. The authors hope that raising awareness of this first reported successful treatment of M. caprae infection in UK domestic cats will aid patient management while mitigating zoonotic risks, and they highlight the oesophagostomy tube used in the first case as a practical aid that reduces stress and supports the owner-caregiver relationship throughout months of therapy.

Subject of Research: Successful treatment of Mycobacterium caprae tuberculosis infection in two domestic cats in the United Kingdom

Article Title: Successful Treatment of Mycobacterium caprae Infection in Two UK Cats

Article References: Clark, E., Gunn‐Moore, D., & O'Halloran, C. (2026). Successful Treatment of Mycobacterium caprae Infection in Two UK Cats. Veterinary Medicine and Science, 12(5), Article e71180. https://doi.org/10.1002/vms3.71180

Image Credits: AI Generated

DOI: 10.1002/vms3.71180

Keywords: Mycobacterium caprae, feline tuberculosis, zoonotic disease, veterinary medicine, triple antibiotic therapy, rifampicin, pradofloxacin, azithromycin, raw meat-based diet, post-tuberculosis lung disease, Mycobacterium tuberculosis complex, UK cats