The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data.

The rapid increase in lipidomic studies has led to a collaborative effort within the community to establish standards and criteria for producing, documenting, and disseminating data. Creating a dynamic easy-to-use checklist that condenses key information about lipidomic experiments into common terminology will enhance the field's consistency, comparability, and repeatability. Here, we describe the structure and rationale of the established Lipidomics Minimal Reporting Checklist to increase transparency in lipidomics research.

Comparing the effects of infant maternal and sibling separation on adolescent behavior in rats (Rattus norvegicus).

Maternal separation in early life has been observed to have lasting, detrimental effects that impair personal and social development and can persist into adulthood. Maternal separation during infancy can be most detrimental during adolescence, leading to long-term adverse effects on development and social behavior. This research study compared the effects of sibling and maternal separation in infancy on anxiety, sociability, or memory later in adolescence (postnatal day, PND, 50-58) in male and female Long-Evans Rats (Rattus norvegicus). Rat pups were semi-randomly assigned into eight conditions for daily isolation (PND 1-14). The groups were separated by the duration of isolation between 15 minutes (control group) or 180 minutes (experimental group) and the sex of the rat. They were also separated by comfort conditions with the dam present in an adjoining cage versus not present and siblings present or not present during isolation. The result was a 2 (15-min vs. 180-min) x 2 (dam vs. no dam) x 2 (single vs. grouped) x 2 (male vs. female) design. Once pups had reached adolescence (PND 50), researchers tested for differences in anxiety, activity, and social behavior using elevated plus-maze, open field habituation, a three-chamber social interaction, and a social discrimination task. Results indicate that longer isolation was more stressful and caused lower body weight. The female rats showed more anxious behavior in the open field but only if they were in the shorter isolation group. Social interaction showed that the rats isolated with the dam had different effects of isolation. In males, shorter isolation with the dam increased sociability but decreased sociability in females. These complicated findings may be due to the effects of inoculation, which describes how moderate stress combined with comfort may produce adaptation or immunity to stress and affect males and females differently.

Complete genome constellation of a dominant Bovine rotavirus genotype circulating in Bangladesh reveals NSP4 intragenic recombination with human strains.

Rotavirus A is a leading cause of non-bacterial gastroenteritis in humans and domesticated animals. Despite the vast diversity of bovine Rotavirus A strains documented in South Asian countries, there are very few whole genomes available for phylogenetic study. A cross-sectional study identified a high prevalence of the G6P[11] genotype of bovine Rotavirus A circulating in the commercial cattle population in Bangladesh. Next-generation sequencing and downstream phylogenetic analysis unveiled all 11 complete gene segments of this strain (BD_ROTA_CVASU), classifying it under the genomic constellation G6P[11]-I2-R2-C2-M2-A13-N2-T6-E2-H3, which belongs to a classical DS-1-like genomic backbone. We found strong evidence of intragenic recombination between human and bovine strains in the Non-structural protein 4 (NSP4) gene, which encodes a multifunctional enterotoxin. Our analyses highlight frequent zoonotic transmissions of rotaviruses in diverse human-animal interfaces, which might have contributed to the evolution and pathogenesis of this dominant genotype circulating in the commercial cattle population in Bangladesh.

MALDI-2-Enabled Oversampling for the Mass Spectrometry Imaging of Metabolites at Single-Cell Resolution.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide valuable insights into the metabolome of complex biological systems such as organ tissues and cells. However, obtaining metabolite data at single-cell spatial resolutions presents a few technological challenges. Generally, spatial resolution is defined by the increment the sample stage moves between laser ablation spots. Stage movements less than the diameter of the focused laser beam (i.e., oversampling) can improve spatial resolution; however, such oversampling conditions result in a reduction in sensitivity. To overcome this, we combine an oversampling approach with laser postionization (MALDI-2), which allows for both higher spatial resolution and improved analyte ionization efficiencies. This approach provides significant enhancements to sensitivity for various metabolite classes (e.g., amino acids, purines, carbohydrates etc.), with mass spectral intensities from 6 to 8 µm pixel sizes (from a laser spot size of ∼13 µm) being commensurate with or higher than those obtained by conventional MALDI at 20 µm pixel sizes for many different metabolites. This technique has been used to map the distribution of metabolites throughout mouse spinal cord tissue to observe how metabolite localizations change throughout specific anatomical regions, such as those distributed to the somatosensory area of the dorsal horn, white matter, gray matter, and ventral horn. Furthermore, this method is utilized for single-cell metabolomics of human iPSC-derived astrocytes at 10 µm pixel sizes whereby many different metabolites, including nucleotides, were detected from individual cells while providing insight into cellular localizations.

Auranofin inhibition of thioredoxin reductase sensitizes lung neuroendocrine tumor cells (NETs) and small cell lung cancer (SCLC) cells to sorafenib as well as inhibiting SCLC xenograft growth.

Thioredoxin Reductase (TrxR) functions to recycle thioredoxin (Trx) during hydroperoxide metabolism mediated by peroxiredoxins and is currently being targeted using the FDA-approved anti-rheumatic drug, auranofin (AF), to selectively sensitize cancer cells to therapy. AF treatment decreased TrxR activity and clonogenic survival in small cell lung cancer (SCLC) cell lines (DMS273 and DMS53) as well as the H727 atypical lung carcinoid cell line. AF treatment also significantly sensitized DMS273 and H727 cell lines in vitro to sorafenib, an FDA-approved multi-kinase inhibitor that depleted intracellular glutathione (GSH). The pharmacokinetic, pharmacodynamic, and safety profile of AF was examined in nude mice with DMS273 xenografts administered AF intraperitoneally at 2 mg/kg or 4 mg/kg (IP) once (QD) or twice daily (BID) for 1-5 d. Plasma levels of AF were 10-20 µM (determined by mass spectrometry of gold), and the optimal inhibition of TrxR activity was obtained at 4 mg/kg once daily, with no effect on glutathione peroxidase 1 activity. This AF treatment extended for 14 d, inhibited TrxR (>75%), and resulted in a significant prolongation of median overall survival from 19 to 23 d (p = .04, N = 30 controls, 28 AF). In this experiment, there were no observed changes in animal bodyweight, complete blood counts (CBCs), bone marrow toxicity, blood urea nitrogen, or creatinine. These results support the hypothesis that AF effectively inhibits TrxR both in vitro and in vivo in SCLC, sensitizes NETs and SCLC to sorafenib, and could be repurposed as an adjuvant therapy with targeted agents that induce disruptions in thiol metabolism.

Novel pathogenic adenovirus in Timneh grey parrot (Psittacus timneh) unveils distinct lineage within Aviadenovirus.

Wild birds harbour a vast diversity of adenoviruses that remain uncharacterised with respect to their genome organisation and evolutionary relatedness within complex host ecosystems. Here, we characterise a novel adenovirus type within Aviadenovirus genus associated with severe necrotising hepatitis in a captive Timneh grey parrot, tentatively named as Timneh grey parrot adenovirus 1 (TpAdV-1). The TpAdV-1 genome is 39,867 bp and encodes 46 putative genes with seven hitherto not described ones. Comparative genomics and phylogenetic analyses revealed highest nucleotide identity with psittacine adenovirus 1 and psittacine adenovirus 4 that formed a discrete monophyletic clade within Aviadenovirus lineage suggesting a deep host co-divergent lineage within Psittaciformes hosts. Several recombination breakpoints were identified within the TpAdV-1 genome, which highlighted an ancient evolutionary relationship across the genera Aviadenovirus, Mastadenovirus and Atadenovirus. This study hints towards a host-adapted sub-lineage of avian adenovirus capable of having significant host virulence in Psittaciformes birds augmented with ecological opportunity.

Myeloperoxidase as a Promising Therapeutic Target after Myocardial Infarction.

Coronary artery disease (CAD) and myocardial infarction (MI) remain leading causes of death and disability worldwide. CAD begins with the formation of atherosclerotic plaques within the intimal layer of the coronary arteries, a process driven by persistent arterial inflammation and oxidation. Myeloperoxidase (MPO), a mammalian haem peroxidase enzyme primarily expressed within neutrophils and monocytes, has been increasingly recognised as a key pro-inflammatory and oxidative enzyme promoting the development of vulnerable coronary atherosclerotic plaques that are prone to rupture, and can precipitate a MI. Mounting evidence also implicates a pathogenic role for MPO in the inflammatory process that follows a MI, which is characterised by the rapid infiltration of activated neutrophils into the damaged myocardium and the release of MPO. Excessive and persistent cardiac inflammation impairs normal cardiac healing post-MI, resulting in adverse cardiac outcomes and poorer long-term cardiac function, and eventually heart failure. This review summarises the evidence for MPO as a significant oxidative enzyme contributing to the inappropriate inflammatory responses driving the progression of CAD and poor cardiac healing after a MI. It also details the proposed mechanisms underlying MPO's pathogenic actions and explores MPO as a novel therapeutic target for the treatment of unstable CAD and cardiac damage post-MI.

The UTHealth Houston Adult Cardiovascular Genomics Certificate Program: Efficacy and Impact on Healthcare Professionals.

Background: The demand for genetic services has outpaced the availability of resources, challenging clinicians untrained in genetic integration into clinical decision-making. The UTHealth Adult Cardiovascular Genomics Certificate (CGC) program trains non-genetic healthcare professionals to recognize, assess, and refer patients with heritable cardiovascular diseases. This asynchronous online course includes 24 modules in three tiers of increasing complexity, using realistic clinical scenarios, interactive dialogues, quizzes, and tests to reinforce learning. We hypothesized that the CGC will increase genomic competencies in this underserved audience and encourage applying genomic concepts in clinical practice. Methods: Required course evaluations include pre- and post-assessments, knowledge checks in each module, and surveys for module-specific feedback. After 6 months, longitudinal feedback surveys gathered data on the long-term impact of the course on clinical practice and conducted focused interviews with learners. Results: The CGC was accredited in September 2022. Principal learners were nurses (24%), nurse practitioners (21%), physicians (16%), and physician assistants. Scores of 283 learners in paired pre- and post-assessments increased specific skills related to recognizing heritable diseases, understanding inheritance patterns, and interpreting genetic tests. Interviews highlighted the CGC's modular structure and linked resources as key strengths. Learners endorsed confidence to use genetic information in clinical practice, such as discussing genetic concepts and risks with patients and referring patients for genetic testing. Learners were highly likely to recommend the CGC to colleagues, citing its role in enhancing heritable disease awareness. Conclusions: The CGC program effectively empowers non-genetic clinicians to master genomic competencies, fostering collaboration to prevent deaths from heritable cardiovascular diseases, and potentially transforming healthcare education and clinical practice.

Functional and perceptive differences between conventional and advanced ankle foot orthoses in community ambulators post-limb trauma: the injuries managed with advanced bracing of the lower extremity (IM ABLE) study.

Introduction: Many military service members and civilians suffer from lower extremity trauma. Despite recent advancements in lower limb bracing technology, it remains unclear whether these newer advanced braces offer improved comfort and functionality compared to conventional options. The IDEO (Intrepid Dynamic Exoskeletal Orthosis), a type of "advanced" orthosis was developed to assist in maintaining high functional performance in patients who have experienced high-energy lower extremity trauma and underwent limb salvage surgeries. Methods: A cross-sector multi-site initiative was completed to study the efficacy of advanced ankle foot orthoses (AFO) for lower limb trauma and injury compared to a conventional AFO. Following fitting, training, and accommodation, the subjects were assessed in each AFO system for mobility, self-reported function, safety and pain, and preference. Results: They preferred the advanced over the conventional AFO and the mobility and exertion perception improved with the advanced AFO with no difference in pain or overall health status scores. Discussion: Thus, an advanced AFO is an option for trauma affecting the lower limb. Long-term studies are required to better understand the accommodation and learning process of using an advanced AFO.

Gape-limited invasive predator frequently kills avian prey that are too large to swallow.

Gape-limited predators (e.g., snakes, many fish) are not generally expected to pose a predation threat to prey that are too large for them to swallow. However, the extent to which snakes predate on prey that exceed their gape limitation remains largely unknown. We conducted the first study to investigate the influence of both prey and predator sizes on the frequency of ingestion success by snakes in a natural system. We combined survival monitoring of an avian prey species (Aplonis opaca) via radio-telemetry with a survey of the size distribution of their major predator (Boiga irregularis) on Guam. This allowed us to assess (1) the frequency of unsuccessful ingestion by the predator, (2) whether the size of the prey predicts ingestion success, (3) whether the size of the predator predicts ingestion success, and (4) the relationship between prey and predator sizes in successful ingestion attempts. We found that nearly half (47.95%) of ingestion attempts by snakes on fledgling birds were unsuccessful, and no instances where unsuccessful ingestion caused the mortality of the snake. Attempts to consume smaller fledglings were as likely to be unsuccessful as attempts to swallow larger fledglings. However, snakes that successfully ingested fledglings were among the largest snakes in the population, and larger than average conspecifics attracted to endothermic prey. The smallest snakes that successfully ingested fledglings attained remarkably high relative prey mass values for their species, consuming prey weighing up to 79.9% of their own mass. Our study indicates that B. irregularis routinely predate prey that are too large for them to successfully ingest, which causes mortality to the prey but poses little risk to the predator. The potential reward for snakes in consuming oversized prey may outweigh the inherent risks, while instances of predation that do not result in consumption may have considerable impacts on prey populations.

Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome.

Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by dnd and ssp gene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possessed dnd or ssp genes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis uncovered several putative new PT synthesis systems, including Type 4 Bacteriophage Exclusion (BREX) brx genes, which were genetically validated in Bacteroides salyersiae. Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessing dnd, ssp, and brx genes revealed 8 PT dinucleotide settings confirmed in 6 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes.

Biosynthesis and differential spatial distribution of the 3-deoxyanthocyanidins apigenidin and luteolinidin at the interface of a plant-cyanobacteria symbiosis exposed to cold.

Aquatic ferns of the genus Azolla (Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N2 in their leaf cavities, Nostoc azollae. Stressed symbioses characteristically turn red due to 3-deoxyanthocyanidin (DA) accumulation, rare in angiosperms and of unknown function. To understand DA accumulation upon cold acclimation and recovery, we integrated laser-desorption-ionization mass-spectrometry-imaging (LDI-MSI), a new Azolla filiculoides genome-assembly and annotation, and dual RNA-sequencing into phenotypic analyses of the symbioses. Azolla sp. Anzali recovered even when cold-induced DA-accumulation was inhibited by abscisic acid. Cyanobacterial filaments generally disappeared upon cold acclimation and Nostoc azollae transcript profiles were unlike those of resting stages formed in cold-resistant sporocarps, yet filaments re-appeared in leaf cavities of newly formed green fronds upon cold-recovery. The high transcript accumulation upon cold acclimation of AfDFR1 encoding a flavanone 4-reductase active in vitro suggested that the enzyme of the first step in the DA-pathway may regulate accumulation of DAs in different tissues. However, LDI-MSI highlighted the necessity to describe metabolite accumulation beyond class assignments as individual DA and caffeoylquinic acid metabolites accumulated differentially. For example, luteolinidin accumulated in epithelial cells, including those lining the leaf cavity, supporting a role for the former in the symbiotic interaction during cold acclimation.

3M™ Defib-Pads as a Reusable Alternative to Commercial Ultrasound Gel in Resource-Limited Settings.

INTRODUCTION: With point-of-care ultrasound (POCUS) use in austere environments comes the challenge of having an ever-available coupling medium for image generation. Commercial gel has numerous drawbacks that can limit its utility in these settings, and no studies have evaluated the potential for a reusable coupling medium. This study aimed to determine whether 3M™ Defib-Pads could be utilized as a reusable alternative to commercial gel for image generation in resource-limited settings. METHODS: A descriptive, cross-sectional survey of Canadian physicians with POCUS interest was conducted to evaluate the interpretability of various POCUS images in a blinded fashion. Three anatomic regions (cardiac, abdominal, and nerve) were utilized, and image generation from the commercial gel and 7 Defib-Pad conditions were evaluated. These included pads that were 1) newly opened, 2) dirtied then rinsed, 3) air dried, 4) rinsed after being air dried, 5) frozen then thawed, 6) used in double thickness, and 7) used with a probe cover. RESULTS: Compared to commercial gel, 3M™ Defib-Pads performed similarly, with adequate image interpretability of up to 100% in some conditions. The exception was pads that had prolonged air exposure, which produced images that were never interpretable. However, subsequent rinsing of these pads with water resulted in restored image generation. CONCLUSION: 3M™ Defib-Pads were found to produce interpretable POCUS images under multiple environmental stressors and with different modalities of use, suggesting that 3M™ Defib-Pads can perform as a reusable gel alternative in resource-limited settings.

Motor Control of Distinct Layer 6 Corticothalamic Feedback Circuits.

Layer 6 corticothalamic (L6 CT) neurons provide massive input to the thalamus, and these feedback connections enable the cortex to influence its own sensory input by modulating thalamic excitability. However, the functional role(s) feedback serves during sensory processing is unclear. One hypothesis is that CT feedback is under the control of extrasensory signals originating from higher-order cortical areas, yet we know nothing about the mechanisms of such control. It is also unclear whether such regulation is specific to CT neurons with distinct thalamic connectivity. Using mice (either sex) combined with in vitro electrophysiology techniques, optogenetics, and retrograde labeling, we describe studies of vibrissal primary motor cortex (vM1) influences on different CT neurons in the vibrissal primary somatosensory cortex (vS1) with distinct intrathalamic axonal projections. We found that vM1 inputs are highly selective, evoking stronger postsynaptic responses in CT neurons projecting to the dual ventral posterior medial nucleus (VPm) and posterior medial nucleus (POm) located in lower L6a than VPm-only-projecting CT cells in upper L6a. A targeted analysis of the specific cells and synapses involved revealed that the greater responsiveness of Dual CT neurons was due to their distinctive intrinsic membrane properties and synaptic mechanisms. These data demonstrate that vS1 has at least two discrete L6 CT subcircuits distinguished by their thalamic projection patterns, intrinsic physiology, and functional connectivity with vM1. Our results also provide insights into how a distinct CT subcircuit may serve specialized roles specific to contextual modulation of tactile-related sensory signals in the somatosensory thalamus during active vibrissa movements.

Functional Dynamics and Selectivity of Two Parallel Corticocortical Pathways from Motor Cortex to Layer 5 Circuits in Somatosensory Cortex.

In the rodent whisker system, active sensing and sensorimotor integration are mediated in part by the dynamic interactions between the motor cortex (M1) and somatosensory cortex (S1). However, understanding these dynamic interactions requires knowledge about the synapses and how specific neurons respond to their input. Here, we combined optogenetics, retrograde labeling, and electrophysiology to characterize the synaptic connections between M1 and layer 5 (L5) intratelencephalic (IT) and pyramidal tract (PT) neurons in S1 of mice (both sexes). We found that M1 synapses onto IT cells displayed modest short-term depression, whereas synapses onto PT neurons showed robust short-term facilitation. Despite M1 inputs to IT cells depressing, their slower kinetics resulted in summation and a response that increased during short trains. In contrast, summation was minimal in PT neurons due to the fast time course of their M1 responses. The functional consequences of this reduced summation, however, were outweighed by the strong facilitation at these M1 synapses, resulting in larger response amplitudes in PT neurons than IT cells during repetitive stimulation. To understand the impact of facilitating M1 inputs on PT output, we paired trains of inputs with single backpropagating action potentials, finding that repetitive M1 activation increased the probability of bursts in PT cells without impacting the time dependence of this coupling. Thus, there are two parallel but dynamically distinct systems of M1 synaptic excitation in L5 of S1, each defined by the short-term dynamics of its synapses, the class of postsynaptic neurons, and how the neurons respond to those inputs.

Complimentary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome.

Monogenic syndromes are associated with neurodevelopmental changes that result in cognitive impairments, neurobehavioral phenotypes including autism and attention deficit hyperactivity disorder (ADHD), and seizures. Limited studies and resources are available to make meaningful headway into the underlying molecular mechanisms that result in these symptoms. One such example is DeSanto-Shinawi Syndrome (DESSH), a rare disorder caused by pathogenic variants in the WAC gene. Individuals with DESSH syndrome exhibit a recognizable craniofacial gestalt, developmental delay/intellectual disability, neurobehavioral symptoms that include autism, ADHD, behavioral difficulties and seizures. However, no thorough studies from a vertebrate model exist to understand how these changes occur. To overcome this, we developed both murine and zebrafish Wac/wac deletion mutants and studied whether their phenotypes recapitulate those described in individuals with DESSH syndrome. We show that the two Wac models exhibit craniofacial and behavioral changes, reminiscent of abnormalities found in DESSH syndrome. In addition, each model revealed impacts to GABAergic neurons and further studies showed that the mouse mutants are susceptible to seizures, changes in brain volumes that are different between sexes and relevant behaviors. Finally, we uncovered transcriptional impacts of Wac loss of function that will pave the way for future molecular studies into DESSH. These studies begin to uncover some biological underpinnings of DESSH syndrome and elucidate the biology of Wac, with advantages in each model.

Improved Signs and Symptoms of Dry Eye Disease for Restasis® Patients Following a Single Tearcare® Treatment: Phase 2 of the SAHARA Study.

Purpose: To evaluate dry eye disease (DED) signs and symptoms six months after a single treatment with Localized Heat Therapy (LHT) (TearCare, Sight Sciences) for patients previously treated for six months with cyclosporine (0.05%) ophthalmic emulsion (CsA) BID (Restasis, Allergan). Setting: Nineteen ophthalmic and optometric practices in 11 US states. Design: Multicenter, cross-over, six month extension to the SAHARA randomized, controlled trial (RCT). Included patients were those randomized to CsA in Phase 1 of the SAHARA RCT. Methods: This was the second phase of the SAHARA RCT in which, following the 6-month endpoint, all patients that had been randomized to CsA discontinued CsA and were treated with LHT and subsequently followed for an additional six months. Outcome measures at 12 months for CsA patients crossed over to LHT included TBUT, OSDI and MGSS. Results: One hundred and sixty-one patients (322 eyes) were analyzed. Mean (SD) baseline TBUT prior to CsA was 4.4 (1.2) seconds, 5.6 (2.6) at 6 months which improved to 6.6 (3.2) and 6.1 (2.8) seconds (both P < 0.001) at 9 and 12 months (3, 6 months post LHT). Mean (SD) OSDI was 50.0 (14.9) at baseline and 34.2 (21.5) after CsA. With LHT at 6 months, this improved to 30.0 (20.6) and 31.0 (19.5) at 9 and 12 months (P = 0.162 vs month 6, P < 0.0001 vs baseline). MGSS was 7.1 (3.2) at baseline, 13.3 (8.2) at the end of CsA treatment which improved to 17.4 (8.8) and 16.1 (9.0) at 9 and 12 months; both P <0.001. Conclusion: SAHARA showed 6-month superiority of LHT to CsA in clinical signs and non-inferiority in symptom scores. This extension shows that patients treated with CsA for 6 months can achieve meaningful additional improvement in signs and symptoms lasting for as long as 6 months following a single LHT treatment without the need for topical prescription therapy.

PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities.

Among dozens of known epigenetic marks, naturally occurring phosphorothioate (PT) DNA modifications are unique in replacing a non-bridging phosphate oxygen with redox-active sulfur and function in prokaryotic restriction-modification and transcriptional regulation. Interest in PTs has grown due to the widespread distribution of the dnd, ssp, and brx genes among bacteria and archaea, as well as the discovery of PTs in 5-10% of gut microbes. Efforts to map PTs in complex microbiomes using existing next-generation and direct sequencing technologies have failed due to poor sensitivity. Here we developed PT-seq as a high-sensitivity method to quantitatively map PTs across genomes and metagenomically identify PT-containing microbes in complex genomic mixtures. Like other methods for mapping PTs in individual genomes, PT-seq exploits targeted DNA strand cleavage at PTs by iodine, followed by sequencing library construction using ligation or template switching approaches. However, PT-specific sequencing reads are dramatically increased by adding steps to heat denature the DNA, block pre-existing 3'-ends, fragment DNA after T-tailing, and enrich iodine-induced breaks using biotin-labeling and streptavidin beads capture. Iterative optimization of the sensitivity and specificity of PT-seq is demonstrated with individual bacteria and human fecal DNA.