The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome

Evidence for HCO3- and NH3/NH4+-dependent pH regulatory mechanisms in the alkaline midgut of the sea urchin larva

Alkaline digestive systems are well described for some insect species and their larval stages. More recently, larvae of the members of ambulacraria superphylum consisting of echinoderms and hemichordates were also discovered to have highly alkaline midguts (pH 9.5-10.5) with the underlying acid-base regulatory mechanisms largely unknown. Using pharmacological inhibition of acid-base transporters in conjunction with ion-selective microelectrode measurements and pH-sensitive dyes, we investigated intracellular and extracellular pH regulatory mechanisms of midgut epithelial cells of a sea urchin (Strongylocentrotus purpuratus) larva. Our findings suggest that vacuolar-type H+-ATPase (inhibited by bafilomycin a1), carbonic anhydrase (inhibited by acetazolamide), anion-exchangers (inhibited by 4,4'-diisothiocyano-2,2'-disulfonic acid or DIDS), and soluble adenylyl cyclase (inhibited by KH7) play crucial roles in cellular acid-base regulation as well as midgut alkalization. Ammonia excretion rates were decreased in the presence of bafilomycin and colchicine, pointing toward vesicular [Formula: see text] trapping and exocytosis mechanism in eliminating nitrogenous proton equivalents from midgut cells. Finally, midgut perfusion studies revealed ouabain-sensitive luminal [Formula: see text] uptake, suggesting a role for Na+/K+-ATPase-mediated ammonia transport in midgut alkalization. This comprehensive pharmacological analysis provides a new working model relying on the CO2/[Formula: see text] and NH3/[Formula: see text] buffer systems for midgut alkalization in the sea urchin larva. These findings are discussed in the context of other alkalizing systems with strong implications for the conserved role of [Formula: see text] and NH3-driven mechanism of midgut alkalization across the animal kingdom.NEW & NOTEWORTHY Sea urchin larvae evolved highly alkaline conditions in their digestive tracts, and the underlying acid-base regulatory mechanisms are little understood. Here we present evidence that the process of luminal alkalization is cAMP-dependent. Furthermore, our data point toward the involvement of bicarbonate and ammonia in regulating midgut fluid pH. These results identified a novel mechanism for luminal alkalization in the digestive tract of a marine animal with strong implications for other alkalizing systems in animals.

Necrophages and necrophiles: a review of their antibacterial defenses and biotechnological potential

With antibiotic resistance on the rise, there is an urgent need for new antibacterial drugs and products to treat or prevent infection. Many such products in current use, for example human and veterinary antibiotics and antimicrobial food preservatives, were discovered and developed from nature. Natural selection acts on all living organisms and the presence of bacterial competitors or pathogens in an environment can favor the evolution of antibacterial adaptations. In this review, we ask if vultures, blow flies and other carrion users might be a good starting point for antibacterial discovery based on the selection pressure they are under from bacterial disease. Dietary details are catalogued for over 600 of these species, bacterial pathogens associated with the diets are described, and an overview of the antibacterial defenses contributing to disease protection is given. Biotechnological applications for these defenses are then discussed, together with challenges facing developers and possible solutions. Examples include use of (a) the antimicrobial peptide (AMP) gene sarcotoxin IA to improve crop resistance to bacterial disease, (b) peptide antibiotics such as serrawettin W2 as antibacterial drug leads, (c) lectins for targeted drug delivery, (d) bioconversion-generated chitin as an antibacterial biomaterial, (e) bacteriocins as antibacterial food preservatives and (f) mutualistic microbiota bacteria as alternatives to antibiotics in animal feed. We show that carrion users encounter a diverse range of bacterial pathogens through their diets and interactions, have evolved many antibacterial defenses, and are a promising source of genes, molecules, and microbes for medical, agricultural, and food industry product development.

The Role of Vulture (Accipitriformes) Cutaneous Microbiota in Infectious Disease Protection

Vultures (Accipitriformes), as obligate scavengers, are regularly exposed to a diverse array of pathogens present in decomposing carcasses. Nevertheless, they exhibit a remarkable ability to resist infections, suggesting a crucial role of skin microbiota in host defense. The microbial communities residing on necrophagic birds' skin create a protective barrier through competitive interactions, antimicrobial compound production, and immunity priming. Additionally, vultures contribute to ecosystem balance by reducing the spread of infectious agents. However, they may also serve as vectors for antimicrobial resistance (AMR) due to their exposure to contaminated food sources. Understanding the dynamics of their microbiota can provide valuable insights into host-microbe interactions, wildlife conservation, and public health. This review examines the composition and functional significance of vulture cutaneous microbiota. Specifically, it explores the role of necrophagic birds' skin microbiota in pathogen exclusion, immune system modulation, and environmental adaptation, with the aim of suggesting further research routes, besides clarifying the ecological implications of such birds.

Intestinal barrier damage caused by addictive substance use disorder

Addictive substance use disorder has a wide range of effects on the intestinal barrier, including damage to the biological, chemical, mechanical, and immune barriers. Damage to the intestinal barrier caused by addictive substance use disorder allows harmful substances and bacteria to cross the intestinal barrier into the circulatory system, leading to systemic inflammatory responses and immune imbalances. In addition, the interaction between the gut flora and the central nervous system is recognized as an important component of the gut-brain axis. Gut barrier damage leads to dysbiosis, which in turn affects brain function by activating immune cells and releasing inflammatory factors. This may lead to altered mood and cognitive function, increased addictive substance cravings, and dependence. Recent research has indicated that reshaping the gut-brain axis and adjusting the composition and abundance of gut microbiota holds promise in alleviating withdrawal symptoms with addictive substance dependence. This article reviews the effects of addictive substance use disorder on the intestinal barrier and explores the possibility of improving addictive substance dependence by treating gut barrier damage.

The costs and benefits of a dynamic host microbiome

All species host a rich community of microbes. This microbiome is dynamic, and displays seasonal, daily, and even hourly changes, but also needs to be resilient to fulfill important roles for the host. In evolutionary ecology, the focus of microbiome dynamism has been on how it can facilitate host adaptation to novel environments. However, an hitherto largely overlooked issue is that the host needs to keep its microbiome in check, which is costly and leads to trade-offs with investing in other fitness-related traits. Investigating these trade-offs in natural vertebrate systems by collecting longitudinal data will lead to deeper insight into the evolutionary mechanisms that shape host-microbiome interactions.

Designing host-associated microbiomes using the consumer/resource model

A key step toward rational microbiome engineering is in silico sampling of realistic microbial communities that correspond to desired host phenotypes, and vice versa. This remains challenging due to a lack of generative models that simultaneously capture compositions of host-associated microbiomes and host phenotypes. To that end, we present a generative model based on the mechanistic consumer/resource (C/R) framework. In the model, variation in microbial ecosystem composition arises due to differences in the availability of effective resources (inferred latent variables), while species' resource preferences remain conserved. Simultaneously, the latent variables are used to model phenotypic states of hosts. In silico microbiomes generated by our model accurately reproduce universal and dataset-specific statistics of bacterial communities. The model allows us to address three salient questions in host-associated microbial ecologies: (i) which host phenotypes maximally constrain the composition of the host-associated microbiomes? (ii) how context-specific are phenotype/microbiome associations, and (iii) what are plausible microbiome compositions that correspond to desired host phenotypes? Our approach aids the analysis and design of microbial communities associated with host phenotypes of interest.

IMPORTANCE

Generative models are extremely popular in modern biology. They have been used to model the variation of protein sequences, entire genomes, and RNA sequencing profiles. Importantly, generative models have been used to extrapolate and interpolate to unobserved regimes of data to design biological systems with desired properties. For example, there has been a boom in machine-learning models aiding in the design of proteins with user-specified structures or functions. Host-associated microbiomes play important roles in animal health and disease, as well as the productivity and environmental footprint of livestock species. However, there are no generative models of host-associated microbiomes. One chief reason is that off-the-shelf machine-learning models are data hungry, and microbiome studies usually deal with large variability and small sample sizes. Moreover, microbiome compositions are heavily context dependent, with characteristics of the host and the abiotic environment leading to distinct patterns in host-microbiome associations. Consequently, off-the-shelf generative modeling has not been successfully applied to microbiomes.To address these challenges, we develop a generative model for host-associated microbiomes derived from the consumer/resource (C/R) framework. This derivation allows us to fit the model to readily available cross-sectional microbiome profile data. Using data from three animal hosts, we show that this mechanistic generative model has several salient features: the model identifies a latent space that represents variables that determine the growth and, therefore, relative abundances of microbial species. Probabilistic modeling of variation in this latent space allows us to generate realistic in silico microbial communities. The model can assign probabilities to microbiomes, thereby allowing us to discriminate between dissimilar ecosystems. Importantly, the model predictively captures host-associated microbiomes and the corresponding hosts' phenotypes, enabling the design of microbial communities associated with user-specified host characteristics.

Host identity drives the assembly of phytoplankton microbiomes across a continental-scale environmental gradient

Host-associated microbiomes often promote host health, yet the key drivers of microbiome assembly and its consequences for host fitness remain unclear. We aimed to determine the relative roles of host identity versus the environment in driving host-microbiome assembly and the consequences of this variation in assembly for host fitness, which may help predict the resilience of host-associated microbiomes and host health amidst fluctuating environmental conditions. Here, we tracked microbiome assembly in association with initially axenic phytoplankton when incubated in seawater originating from four nearshore locations along a continental-scale environmental gradient of North America. Microbiome assembly was highly deterministic. Unexpectedly, host species identity was the overwhelming driver of microbiome community assembly despite continental-scale variation in the environment. Although secondary to host identity, the environment was a significant driver of microbiome assembly for each species evaluated, which, in turn, conferred cascading effects on host fitness as shown by thermal tolerance growth assays. We also found that host-specific microbiomes had host-specific fitness effects, particularly under thermally stressful conditions. Overall, our results advance our understanding of microbiome assembly by empirically demonstrating that although variation among host microbiomes imparted by the local environment has significant implications for host health, the host species is the overwhelming driver of microbiome assembly regardless of wide-scale variation in the environment.

High-fidelity imaging of drug-induced acute gastritis by using a fluorescent and photoacoustic dual-modal probe with good stability in stomach acid

In consideration of deep tissue imaging and signal fidelity, fluorescent-photoacoustic (PA) dual-modal probes are much more desirable. However, dual-modal imaging of gastritis using molecular probes remains a challenge due to the harsh gastric acid environment in the stomach. Based on the positive correlation between gastritis and cell viscosity, stomach acid-stable and viscosity-activated probes could potentially diagnose gastritis. As a proof of concept, herein, a fluorescent and photoacoustic dual-modal probe (named WSP-1) is revealed for the imaging of drug-induced acute gastritis in vivo. WSP-1 exhibits viscosity-dependent fluorescence emission and photoacoustic signals. A rotatable C-C single bond is incorporated into the D-π-A structure of WSP-1, which could facilitate the formation of the twisted intramolecular charge transfer (TICT) state in a low-viscosity environment (weak fluorescence/PA signal) and the intramolecular charge transfer (ICT) state in a high-viscosity environment (strong fluorescence/PA signal). WSP-1 has demonstrated the capability to target mitochondria and can be utilized to monitor the viscosity enhancement of cells during inflammation. Most importantly, WSP-1 exhibits good optical and structural stability in gastric acid. By leveraging these desirable features of WSP-1, we have achieved fluorescent and 3D photoacoustic in situ imaging of drug-induced acute gastritis following oral administration of WSP-1.

In vitro bioaccessibility of cyclodi-BADGE present in canned seafood: A new approach for the estimation of dietary exposure of the Spanish population

Human dietary exposure to chemical compounds is a priority issue for public health authorities since it constitutes a key step in risk assessment, and food packaging could be an important source of contamination. In this study, the bioaccessibility of cyclodi-BADGE was evaluated in canned seafood samples using a standardized protocol of in vitro gastrointestinal digestion and an analytical method based on liquid chromatography coupled to tandem mass spectrometry. The impact of enzymes, different gastric pHs, and food-covering liquids on the bioaccessibility of cyclodi-BADGE was studied. The results highlighted that cyclodi-BADGE was available to be absorbed at the intestinal level (90.9-112.3%), and its bioaccessibility increased substantially in fat food samples. Finally, the estimated dietary exposure to cyclodi-BADGE in the Spanish adult population reached values of 14.26 μg/kg bw/day for tuna in tomato, exceeding the tolerable daily intake (1.5 μg/kg bw/day) recommended for chemicals with high toxicological risk.

Preliminary In Vitro Assessment of Whey Protein Isolate Hydrogel with Cannabidiol as a Potential Hydrophobic Oral Drug Delivery System for Colorectal Cancer Therapy

Colorectal cancer (CRC) is the second global cause of cancer morbidity. Often, potent CRC drugs fail to reach the market, due to the molecule having low solubility levels. Therefore, there is a need to develop a viable, targeted delivery system for hydrophobic drugs. Whey protein isolate (WPI), in the form of hydrogels, has demonstrated loadability with hydrophobic molecules. Hydrophobic cannabidiol (CBD) has demonstrated potential in inhibiting and suppressing CRC tumour growth. Therefore, in this study, WPI hydrogels were assessed as a novel oral hydrophobic drug delivery vehicle, using CBD as a model drug. The hydrogels were analysed in conditions consistent with the alimentary tract. The investigation was performed at pH 2 (stomach), pH 7 (small intestines) and pH 9 (large intestines) and using the enzymes pepsin (stomach) and protease (small and large intestines) to simulate the digestive environment. Polymer swelling assays demonstrated that the swelling potential of the hydrogels was strongly dependent on pH. At pH 2, hydrogels decreased in mass, losing around 10% of their initial mass, while hydrogels in a pH 9 environment increased in mass by approximately 50%. However, the enzymatic degradation of the hydrogels at pH 2 (pepsin, stomach), pH 7 (protease, small intestines) and pH 9 (protease, large intestines) was more pronounced in the neutral-alkaline pH range. Pepsin at pH 2 had no significant effect on the hydrogels. In contrast, protease at pH 9 significantly degraded the hydrogels, resulting in a mass loss of 30-40% from the initial mass. The results suggesting a higher rate of degradation in the intestines rather than in the stomach. Furthermore, CBD release, analysed with U.V. spectroscopy, demonstrated a higher release rate in pH conditions associated with the intestines (pH 7 and pH 9) rather than the stomach (pH 2), suggesting a higher rate of CBD release in regions of the digestive tract affected by CRC. Significantly, the hydrogels significantly reduced the viability of HT29 CRC cells. This study demonstrates the potential of the utilisation of WPI hydrogels as an oral hydrophobic drug delivery system.

In Vitro Acid Resistance of Pathogenic Candida Species in Simulated Gastric Fluid

Background and Aims

Although species in the fungal genus Candida are often commensal residents of the gastrointestinal (GI) tract, they can also cause high-mortality systemic candidiasis. Most pathogenic Candida species are dimorphic fungi that exist predominantly in filamentous forms in the invading tissues. Candida albicans is the most prominent pathogen among Candida species, but nonalbicans Candida species have also emerged as important pathogens. The stomach is the most acidic niche in the GI tract and is maintained at pH 1-2 in healthy individuals. The aim of the present study was to determine whether Candida species can survive in gastric fluid and to observe their morphology under varied pH conditions.

Methods

We investigated the in vitro survival of the pathogenic Candida species C. albicans, Candida glabrata, Candida parapsilosis, and Candida tropicalis in simulated gastric fluid.

Results

We first described that a portion of the 4 Candida species can survive under highly acidic conditions. Moreover, dimorphic Candida species, namely, C. albicans, C. parapsilosis, and C. tropicalis, exhibited yeast-hyphal transition in simulated gastric fluid with elevated pH. Pathogenic filamentous cells had lower acid resistance than yeast cells.

Conclusion

These findings may illuminate the migration to the lower GI tract by commensal fungi of the oral cavity.

Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile

Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.

Precise photothermal treatment of bacterial infection mediated by charge-switchable nanoplatform with acylsulfonamide betaine surface

Photothermal therapy (PTT) offers a promising approach for the treatment of drug-resistant bacterial-infected wounds, yet it requires precise targeting of thermal damage to bacteria rather than healthy tissues. Herein, ultrasmall CuS NPs modified with polyzwitterion containing acylsulfonamide betaine (PCBSA@CuS), which provides a sensitive and reversible charge conversion around pH 6.8, are used to enhance the healing of bacteria-infected wounds. In the acidic infection microenvironment, the majority of PCBSA@CuS can electrostatically adsorb onto bacterial cells through cationic exposure, resulting in direct damage and death of bacteria upon NIR irradiation. Additionally, the photothermal NPs rapidly return to a zwitterionic nature in normal physiological environments, ensuring lower affinity and avoiding thermal damage to healthy tissues during continuous PTT. Compared to inert photothermal systems such as PEG-modified CuS NPs, the NPs used in this study exhibited higher bactericidal and wound healing efficacy. Therefore, this nano-antibacterial agent with highly sensitive thermal-targeting function provides a novel photothermal strategy for efficient and biosafe treatment of infected wounds.

Nanoparticle-Mediated Delivery of Deferasirox: A Promising Strategy Against Invasive Aspergillosis

BACKGROUND

Invasive aspergillosis (IA) is a deadly fungal lung infection. Antifungal resistance and treatment side effects are major concerns. Iron chelators are vital for IA management, but systemic use can cause side effects. We developed nanoparticles (NPs) to selectively deliver the iron chelator deferasirox (DFX) for IA treatment.

METHODS

DFX was encapsulated in poly(lactic-co-glycolic acid) (PLGA) NPs using a single emulsion solvent evaporation method. The NPs were characterized by light scattering and electron microscopy. DFX loading efficiency and release were assessed spectrophotometrically. Toxicity was evaluated using SRB, luciferase, and XTT assays. Therapeutic efficacy was tested in an IA mouse model, assessing fungal burden by qPCR and biodistribution via imaging.

RESULTS

DFX-NPs had a size of ~50 nm and a charge of ~-30 mV, with a loading efficiency of ~80%. Release kinetics showed DFX release via diffusion and bioerosion. The EC50 of DFX-NPs was significantly lower (p < 0.001) than the free drug, and they were significantly less toxic (p < 0.0001) in mammalian cell cultures. In vivo, NP treatment significantly reduced Af burden (p < 0.05).

CONCLUSION

The designed DFX-NPs effectively target and kill Af with minimal toxicity to mammalian cells. The significant in vivo therapeutic efficacy suggests these NPs could be a safe and effective treatment for IA.

Characterizing Biomarkers of Continuous Peristalsis and Bolus Transit During Oral Feeding in Infants at pH-Impedance Evaluation: Clinical and Research Implications

OBJECTIVE

To examine the biomarkers of pharyngoesophageal swallowing during oral feeding sessions in infants undergoing pH-impedance testing and determine whether swallow frequencies are distinct between oral-fed and partially oral-fed infants.

STUDY DESIGN

One oral feeding session was performed in 40 infants during pH-impedance studies and measurements included swallowing frequency, multiple swallow rate, air and liquid swallow rates, esophageal swallow clearance time, and gastroesophageal reflux (GER) characteristics. Linear and mixed statistical models were applied to examine the swallowing markers and outcomes.

RESULTS

Infants (30.2 ± 4.4 weeks' birth gestation) were evaluated at 41.2 ± 0.4 weeks' postmenstrual age. Overall, 10 675 swallows were analyzed during the oral feeding sessions (19.3 ± 5.4 minutes per infant) and GER events were noted (2.5 ± 0.3 per study). Twenty-four-hour acid reflux index (ARI) was 9.5 ± 2.0%. Differences were noted in oral-fed and partially oral-fed infants for volume consumption (P < .01), consumption rate (P < .01), and length of hospital stay in days (P < .01). Infants with ARI >7% had greater frequency of swallows (P = .01). The oral-fed group had greater ARI (12.7 ± 3.3%, P = .05).

CONCLUSIONS

Oropharyngeal swallowing regulatory characteristics decrease over the feeding duration and were different between ARI >7% vs ≤7%. Although GER is less in infants who are partially oral-fed, the neonates with increased acid exposure achieved greater oral intakes and shorter hospitalizations, despite the presence of comorbidities. Pharyngoesophageal stimulation as during consistent feeding or GER events can activate peristaltic responses and rhythms, which may be contributory to the findings.

From the inside out: Were the cuticular Pseudonocardia bacteria of fungus-farming ants originally domesticated as gut symbionts?

The mutualistic interaction specificity between attine ants and antibiotic-producing Actinobacteria has been controversial because Pseudonocardia strains cannot always be isolated from worker cuticles across attine ant species, while other actinobacteria can apparently replace Pseudonocardia and also inhibit growth of Escovopsis mycopathogens. Here we report that across field samples of Panamanian species: (i) Cuticular Pseudonocardia were largely restricted to species in the crown of the attine phylogeny and their appearance likely coincided with the first attines colonizing Central/North America. (ii) The phylogenetically basal attines almost always had cuticular associations with other Actinobacteria than Pseudonocardia. (iii) The sub-cuticular glands nourishing cuticular bacteria appear to be homologous throughout the phylogeny, consistent with an ancient general attine-Actinobacteria association. (iv) The basal attine species investigated always had Pseudonocardia as gut symbionts while Pseudonocardia presence appeared mutually exclusive between cuticular and gut microbiomes. (v) Gut-associated Pseudonocardia were phylogenetically ancestral while cuticular symbionts formed a derived crown group within the Pseudonocardia phylogeny. We further show that laboratory colonies often secondarily acquire cuticular Actinobacteria that they do not associate with in the field, suggesting that many previous studies were uninformative for questions of co-adaptation in the wild. An exhaustive literature survey showed that published studies concur with our present results, provided that they analyzed field colonies and that Actinobacteria were specifically isolated from worker cuticles shortly after field collection. Our results offer several testable hypotheses for a better overall understanding of attine-Pseudonocardia interaction dynamics and putative coevolution throughout the Americas.

Assessing food digestion in the elderly using in vitro gastrointestinal models

With the global population of individuals aged 65 and older projected to exceed 1.5 billion by 2050, understanding the impact of aging on digestion and nutrient absorption is essential for addressing the nutritional needs of the elderly. This review explores the limitations of traditional in vivo studies and underscores the growing importance of in vitro gastrointestinal models as an ethical and cost-effective alternative for investigating digestion in the elderly. The review provides a comprehensive analysis of age-related physiological changes in the gastrointestinal tract (GIT), and critically evaluates how static and dynamic in vitro models have been adapted to simulate these changes. We also discuss the significant challenges these models face in accurately replicating the complexities of elderly digestion, particularly in mimicking the interactions between digestive processes and the gut microbiome. By addressing these challenges, particularly through the development of more physiologically relevant and personalized in vitro models, this review highlights the potential to enhance our understanding of elderly digestion and improve nutritional strategies, ultimately contributing to better health outcomes for the aging population.

Effect of supplemental milk replacer and liquid starter diet for 4 and 11 days postweaning on intestinal parameters of weaned piglets and growth to slaughter

Reduced piglet feed intake immediately postweaning (pw) leads to disruption of small intestine structure and function and reduced growth. Our objective was to evaluate the effect of providing supplemental milk or liquid starter diet for either 4 or 11 days pw, on intestinal parameters of newly weaned piglets and growth to slaughter. At weaning (28 ± 0.6 days old), five hundred and eighty-seven piglets ((Large White × Landrace) × Duroc) were divided into 59 pen groups, each containing 9-10 same sex (entire male or female) piglets. The pen groups were blocked by sex and weaning weight and provided with ad-libitum access to one of five dietary treatments: (1) Dry pelleted starter diet (control; CON); (2) CON+liquid milk replacer for 4 days pw (M4); (3) CON+liquid milk replacer for 11 days pw (M11); (4) CON+liquid starter diet for 4 days pw (S4) and (5) CON+liquid starter diet for 11 days pw (S11). Pen groups were weighed at weaning, days 11, 20, 28, and 47 pw and at target sale weight. Feed disappearance (on a DM basis) was recorded on each weighing day. On day 7 pw, 10 piglets per treatment were euthanised to collect small intestine tissue samples for determination of villus height (VH), crypt depth and brush-border membrane enzyme activity. Data were analysed using SAS-version 9.4. Between days 0 and 11 pw, M11 increased average daily feed intake by 48% and average daily gain (ADG) by 57% compared to CON (P < 0.05), and increased ADG by 54% (P < 0.05) compared to S4. Piglets on M11 also had improved feed conversion efficiency compared with CON piglets between days 0 and 11 pw. Treatment did not affect growth performance after day 28 pw, or carcass parameters at slaughter. At day 7 pw, M11 piglets had 37% higher jejunal VH than CON piglets (P < 0.05) and S11 piglets had 28% higher ileal VH than S4 piglets (P < 0.05). M11 piglets had up to 150% higher ileal sucrase activity than M4, S4 and S11 piglets (P < 0.05) and 180% higher ileal maltase activity than S4 piglets (P < 0.05). In conclusion, M11 reduced the immediate negative effects of weaning, as it was associated with increased feed intake, growth, brush-border membrane enzyme activity and improved intestinal structure early pw. However, there were no carryover effects of any of the liquid supplements on growth or feed efficiency or carcass weight at slaughter.

Gastric stability of bare and chitosan-fabricated ferritin and its bio-mineral: implication for potential dietary iron supplements

Iron deficiency anaemia (IDA), the most widespread nutritional disorder, is a persistent global health issue affecting millions, especially in resource-limited geographies. Oral iron supplementation is usually the first choice for exogenous iron administration owing to its convenience, effectiveness and low cost. However, commercially available iron supplementations are often associated with oxidative stress, gastrointestinal side effects, infections and solubility issues. Herein, we aim to address these limitations by employing ferritin proteins-self-assembled nanocaged architectures functioning as a soluble cellular iron repository-as a non-toxic and biocompatible alternative. Our in vitro studies based on PAGE and TEM indicate that bare ferritin proteins are resistant to gastric conditions but their cage integrity is compromised under longer incubation periods and at higher concentrations of pepsin, which is a critical component of gastric juice. To ensure the safe delivery of encapsulated iron cargo, with minimal cage disintegration/degradation and iron leakage along the gastrointestinal tract, we fabricated the surface of ferritin with chitosan. Further, the stoichiometry and absorptivity of iron-chelator complexes at both gastric and circumneutral pH were estimated using Job's plot. Unlike bipyridyl, deferiprone exhibited pH dependency. In vitro kinetics was studied to evaluate iron release from bare and chitosan-fabricated ferritins employing both reductive (in the presence of ascorbate and bipyridyl) and non-reductive (direct chelation by deferiprone) pathways to determine their bio-mineral stabilities. Chitosan-decorated ferritin displayed superior cage integrity and iron retention capability over bare ferritin in simulated gastric fluid. The ability of ferritins to naturally facilitate controlled iron release in conjugation with enteric coating provided by chitosan may mitigate the aforementioned side effects and enhance iron absorption in the intestine. The results of the current study could pave the way for the development of an oral formulation based on ferritin-caged iron bio-mineral that can be a promising alternative for the treatment of IDA, offering better therapeutic outcomes.

Host control of the microbiome: Mechanisms, evolution, and disease

Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.

Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen

Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.

Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli

Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g., in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e., they are induced under mild acid stress but not under severe acid stress. However, it was not known to what extent fine-tuned expression of motility genes is related to fitness and the ability to survive periods of acid shock. In this study, we demonstrate that the expression of FlhDC, the master regulator of flagellation, is inversely correlated with the acid shock survival of E. coli. We encountered this phenomenon when analyzing mutants from the Keio collection, in which the expression of flhDC was altered by an insertion sequence element. These results suggest a fitness trade-off between acid tolerance and motility.IMPORTANCEEscherichia coli is extremely acid-resistant, which is crucial for survival in the gastrointestinal tract of vertebrates. Recently, we systematically studied the response of E. coli to mild and severe acidic conditions using Ribo-Seq and RNA-Seq. We found that motility genes are induced at pH 5.8 but not at pH 4.4, indicating stress-dependent synthesis of flagellar components. In this study, we demonstrate that motility-activating mutations upstream of flhDC, encoding the master regulator of flagella genes, reduce the ability of E. coli to survive periods of acid shock. Furthermore, we show an inverse correlation between motility and acid survival using a chromosomal isopropyl β-D-thio-galactopyranoside (IPTG)-inducible flhDC promoter and by sampling differentially motile subpopulations from swim agar plates. These results reveal a previously undiscovered trade-off between motility and acid tolerance and suggest a differentiation of E. coli into motile and acid-tolerant subpopulations, driven by the integration of insertion sequence elements.

Enterococcus faecalis provides protection during scavenging in carrion crow ( Corvus corone)

The gut microbiota significantly influences host physiology and provides essential ecosystem services. While diet can affect the composition of the gut microbiota, the gut microbiota can also help the host adapt to specific dietary habits. The carrion crow ( Corvus corone), an urban facultative scavenger bird, hosts an abundance of pathogens due to its scavenging behavior. Despite this, carrion crows infrequently exhibit illness, a phenomenon related to their unique physiological adaptability. At present, however, the role of the gut microbiota remains incompletely understood. In this study, we performed a comparative analysis using 16S rRNA amplicon sequencing technology to assess colonic content in carrion crows and 16 other bird species with different diets in Beijing, China. Our findings revealed that the dominant gut microbiota in carrion crows was primarily composed of Proteobacteria (75.51%) and Firmicutes (22.37%). Significant differences were observed in the relative abundance of Enterococcus faecalis among groups, highlighting its potential as a biomarker of facultative scavenging behavior in carrion crows. Subsequently, E. faecalis isolated from carrion crows was transplanted into model mice to explore the protective effects of this bacterial community against Salmonella enterica infection. Results showed that E. faecalis down-regulated the expression of pro-inflammatory cytokines tumor necrosis factor alpha (TNF-α), interferon gamma (IFN-γ), and interleukin 6 (IL-6), prevented S. enterica colonization, and regulated the composition of gut microbiota in mice, thereby modulating the host's immune regulatory capacity. Therefore, E. faecalis exerts immunoregulatory and anti-pathogenic functions in carrion crows engaged in scavenging behavior, offering a representative case of how the gut microbiota contributes to the protection of hosts with specialized diets.

Interspecies scaling of toxicity reference values in human health versus ecological risk assessments: A critical review

Risk assessments that focus on anthropogenic chemicals in environmental media-whether considering human health or ecological effects-often rely on toxicity data from experimentally studied species to estimate safe exposures for species that lack similar data. Current default extrapolation approaches used in both human health risk assessments and ecological risk assessments (ERAs) account for differences in body weight between the test organisms and the species of interest, but the two default approaches differ in important ways. Human health risk assessments currently employ a default based on body weight raised to the three-quarters power. Ecological risk assessments for wildlife (i.e., mammals and birds) are typically based directly on body weight, as measured in the test organism and receptor species. This review describes differences in the experimental data underlying these default practices and discusses the many factors that affect interspecies variability in chemical exposures. The interplay of these different factors can lead to substantial departures from default expectations. Alternative methodologies for conducting more accurate interspecies extrapolations in ERAs for wildlife are discussed, including tissue-based toxicity reference values, physiologically based toxicokinetic and/or toxicodynamic modeling, chemical read-across, and a system of categorical defaults based on route of exposure and toxic mode of action. Integr Environ Assess Manag 2024;20:749-764. © 2023 SETAC.

Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is associated with altered gut microbiota; however, there has been a focus on fecal samples, which are not representative of the entire digestive tract. Mucosal biopsies of the descending duodenum were collected. Five regions of the 16S rRNA gene were amplified and sequenced. Other assessments conducted on the study subjects included body mass index, transient elastography, liver enzymes, and lipid profile. Fifty-one subjects (36 with MASLD and 15 controls) were evaluated. There was no significant difference between the two groups regarding alpha- or beta-diversity of the duodenal mucosal microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the genera Serratia and Aggregatibacter were more abundant in the duodenal mucosa of patients with MASLD, whereas the duodenal mucosal microbiota of the healthy controls was enriched with the genus Petrobacter. PICRUSt2 analysis revealed that genes associated with amino acid degradation and carboxylate degradation were significantly enriched in the duodenal mucosal microbiota of patients with MASLD. Our findings reveal the duodenal mucosal microbiota in patients with MASLD, which could contribute to future studies investigating the causal relationship between duodenal microbiota and MASLD.

Integrating microbiome science and evolutionary medicine into animal health and conservation

Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.

Effect of dietary calcium source, exogenous phytase, and formic acid on inositol phosphate degradation, mineral and amino acid digestibility, and microbiota in growing pigs

The choice of the calcium (Ca) source in pig diets and the addition of formic acid may affect the gastrointestinal inositol phosphate (InsP) degradation and thereby, phosphorus (P) digestibility in pigs. This study assessed the effects of different Ca sources (Ca carbonate, Ca formate), exogenous phytase, and chemical acidification on InsP degradation, nutrient digestion and retention, blood metabolites, and microbiota composition in growing pigs. In a randomized design, 8 ileal-cannulated barrows (24 kg initial BW) were fed 5 diets containing Ca formate or Ca carbonate as the only mineral Ca addition, with or without 1,500 FTU/kg of an exogenous hybrid 6-phytase. A fifth diet was composed of Ca carbonate with phytase but with 8 g formic acid/kg diet. No mineral P was added to the diets. Prececal InsP6 disappearance and P digestibility were lower (P ≤ 0.032) in pigs fed diets containing Ca formate. In the presence of exogenous phytase, InsP5 and InsP4 concentrations in the ileal digesta were lower (P ≤ 0.019) with Ca carbonate than Ca formate. The addition of formic acid to Ca carbonate with phytase diet resulted in greater (P = 0.027) prececal InsP6 disappearance (87% vs. 80%), lower (P = 0.001) InsP5 concentration, and greater (P ≤ 0.031) InsP2 and myo-inositol concentrations in the ileal digesta. Prececal P digestibility was greater (P = 0.004) with the addition of formic acid compared to Ca carbonate with phytase alone. Prececal amino acid (AA) digestibility of some AA was greater with Ca formate compared to Ca carbonate but only in diets with phytase (P ≤ 0.048). The addition of formic acid to the diet with Ca carbonate and phytase increased (P ≤ 0.006) the prececal AA digestibility of most indispensable AA. Exogenous phytase affected more microbial genera in the feces when Ca formate was used compared to Ca carbonate. In the ileal digesta, the Ca carbonate diet supplemented with formic acid and phytase led to a similar microbial community as the Ca formate diets. In conclusion, Ca formate reduced prececal InsP6 degradation and P digestibility, but might be of advantage in regard to prececal AA digestibility in pigs compared to Ca carbonate when exogenous phytase is added. The addition of formic acid to Ca carbonate with phytase, however, resulted in greater InsP6 disappearance, P and AA digestibility values, and changed ileal microbiota composition compared to Ca carbonate with phytase alone.

Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes

Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.

Incremental increases in physiological fluid shear progressively alter pathogenic phenotypes and gene expression in multidrug resistant Salmonella

The ability of bacteria to sense and respond to mechanical forces has important implications for pathogens during infection, as they experience wide fluid shear fluctuations in the host. However, little is known about how mechanical forces encountered in the infected host drive microbial pathogenesis. Herein, we combined mathematical modeling with hydrodynamic bacterial culture to profile transcriptomic and pathogenesis-related phenotypes of multidrug resistant S. Typhimurium (ST313 D23580) under different fluid shear conditions relevant to its transition from the intestinal tract to the bloodstream. We report that D23580 exhibited incremental changes in transcriptomic profiles that correlated with its pathogenic phenotypes in response to these progressive increases in fluid shear. This is the first demonstration that incremental changes in fluid shear forces alter stress responses and gene expression in any ST313 strain and offers mechanistic insight into how forces encountered by bacteria during infection might impact their disease-causing ability in unexpected ways.

Opportunistic meat-eating by urban folivorous-frugivorous monkeys

The consumption of vertebrate tissues and eggs (hereinafter "meat") is relatively common among some primates that are highly frugivorous or eclectic omnivores, but rare or absent in those that are highly folivorous. The Neotropical howler monkeys (Alouatta spp.) belong in the latter group. Here we report the consumption of meat by free-ranging urban black and gold howler monkeys (Alouatta caraya) and discuss the potential role of the consumed meat as a source of energy, protein, or micronutrients. We studied three groups of howler monkeys (comprising four to seven individuals), living in city squares (0.6, 1.5, and 1.9 ha) in south Brazil, from July 2022 to May 2023 (65 days; 797 h of observations). All of the study groups were spontaneously supplemented daily by people with variable amounts and types of food provided. Meat was only offered in the two larger squares. The groups' diets included leaves (42-49% scan sampling feeding records), fruit (3-20%), and flowers (2-5%) from 13 to 20 plant species, and considerable amounts of supplemented food (27-50%). We recorded 33 individual events of ingestion of supplemented cooked meat, three individual events of dove egg predation, and three bird nest inspections without egg consumption. All members of the two groups in the larger squares, except an infant male, ingested meat at least once. Meat accounted for 1% of total scan feeding records of both groups with access to this supplement. We conclude that whereas the opportunistic consumption of meat probably contributed only minor amounts of energy and protein to the study subjects, it may have benefitted them with micronutrients that are scarce in plant foods.

The effect of host admixture on wild house mouse gut microbiota is weak when accounting for spatial autocorrelation

The question of how interactions between the gut microbiome and vertebrate hosts contribute to host adaptation and speciation is one of the major problems in current evolutionary research. Using bacteriome and mycobiome metabarcoding, we examined how these two components of the gut microbiota vary with the degree of host admixture in secondary contact between two house mouse subspecies (Mus musculus musculus and M. m. domesticus). We used a large data set collected at two replicates of the hybrid zone and model-based statistical analyses to ensure the robustness of our results. Assuming that the microbiota of wild hosts suffers from spatial autocorrelation, we directly compared the results of statistical models that were spatially naive with those that accounted for spatial autocorrelation. We showed that neglecting spatial autocorrelation can strongly affect the results and lead to misleading conclusions. The spatial analyses showed little difference between subspecies, both in microbiome composition and in individual bacterial lineages. Similarly, the degree of admixture had minimal effects on the gut bacteriome and mycobiome and was caused by changes in a few microbial lineages that correspond to the common symbionts of free-living house mice. In contrast to previous studies, these data do not support the hypothesis that the microbiota plays an important role in host reproductive isolation in this particular model system.

Ascorbate mediates the non-enzymatic reduction of nitrite to nitric oxide

Nitric oxide (NO•) generated by nitric oxide synthases is involved in many physiological and pathophysiological processes. However, non-enzymatic formation of NO• also occurs in vivo. Here we investigated the production of NO• from nitrite, as facilitated by ascorbate, over the pH range of 2.4-7.4. Using a nitric oxide electrode, we observed at low pH a rapid generation of NO• from nitrite and ascorbate that slows with increasing pH. The formation of NO• was confirmed by its reaction with oxyhemoglobin. In the ascorbate/nitrite system a steady-state level of NO• was achieved, suggesting that a futile redox cycle of nitrite-reduction by ascorbate and NO•-oxidation by dioxygen was established. However, at pH-values of around 7 and greater, the direct reduction of nitrite by ascorbate is very slow; thus, this route to the non-enzymatic production of NO• is not likely to be significant process in vivo in environments having a pH around 7.4. The production of nitric oxide by nitrite and ascorbate would be important only in areas of lower pH, e.g. stomach/digestive system, sites of inflammation, and areas of hypoxia such as tumor tissue. In patients receiving very large doses of ascorbate delivered by intravenous infusion, plasma levels of ascorbate on the order of 20 - 30 mM can be achieved. After infusion, levels of nitrate and nitrite in plasma were unchanged. Thus, in blood and tissue that maintain a pH of about 7.4, the reduction of nitrite to nitric oxide by ascorbate appears to be insignificant, even at very large, pharmacological levels of ascorbate.

Unveiling the Role of Nonionic Surfactants in Enhancing Cefotaxime Drug Solubility: A UV-Visible Spectroscopic Investigation in Single and Mixed Micellar Formulations

This study reports the interfacial phenomenon of cefotaxime in combination with nonionic surfactants, Triton X-100 (TX-100) and Tween-80 (TW-80), and their mixed micellar formulations. Cefotaxime was enclosed in a micellar system to improve its solubility and effectiveness. TX-100 and TW-80 were used in an amphiphilic self-assembly process to create the micellar formulation. The effect of the addition of TX-100, a nonionic surfactant, on the ability of TW-80 to solubilize the drug was examined. The values of the critical micelle concentration (CMC) were determined via UV-Visible spectroscopy. Gibbs free energies (ΔGp and ΔGb), the partition coefficient (Kx), and the binding constant (Kb) were also computed. In a single micellar system, the partition coefficient (Kx) was found to be 33.78 × 106 and 2.78 × 106 in the presence of TX-100 and TW-80, respectively. In a mixed micellar system, the value of the partition coefficient for the CEF/TW-80 system is maximum (5.48 × 106) in the presence of 0.0019 mM of TX-100, which shows that TX-100 significantly enhances the solubilizing power of micelles. It has been demonstrated that these surfactants are effective in enhancing the solubility and bioavailability of therapeutic compounds. This study elaborates on the physicochemical characteristics and solubilization of reactive drugs in single and mixed micellar media. This investigation, conducted in the presence of surfactants, shows a large contribution to the binding process via both hydrogen bonding and hydrophobic interactions.

An Alkaline Foregut Protects Herbivores from Latex in Forage, but Increases Their Susceptibility to Bt Endotoxin

About 10% of angiosperms, an estimated 20,000 species, produce latex from ubiquitous isoprene precursors. Latex, an aqueous suspension of rubber particles and other compounds, functions as an antifeedant and herbivory deterrent. It is soluble in neutral to alkaline pH, and coagulates in acidic environments. Here, I propose that foregut-fermenting herbivores such as ruminants, kangaroos, sloths, insect larvae, and tadpoles have adapted to latex in forage with the evolution of alkaline anterior digestive chamber(s). However, they consequently become susceptible to the action of Bacillus thuringiensis (Bt) δ-endotoxin and related bioinsecticides which are activated in alkaline environments. By contrast, hindgut-fermenting herbivores, such as horses and rabbits, have acidic anterior digestive chambers, in which latex coagulates and may cause gut blockage, but in which Bt is not activated. The latex-adapted foregut herbivore vs. latex-maladapted hindgut herbivore hypothesis developed in this paper has implications for hindgut-fermenting livestock and zoo animals which may be provided with latex-containing forage that is detrimental to their gut health. Further, ruminants and herbivorous tadpoles with alkaline anterior chambers are at risk of damage by the supposedly "environmentally friendly" Bt bioinsecticide, which is widely disseminated or engineered into crops which may enter animal feed streams.

Oral enzyme therapy for maple syrup urine disease (MSUD) suppresses plasma leucine levels in intermediate MSUD mice and healthy nonhuman primates

Maple syrup urine disease (MSUD) is an inborn error of branched-chain amino acid metabolism affecting several thousand individuals worldwide. MSUD patients have elevated levels of plasma leucine and its metabolic product α-ketoisocaproate (KIC), which can lead to severe neurotoxicity, coma, and death. Patients must maintain a strict diet of protein restriction and medical formula, and periods of noncompliance or illness can lead to acute metabolic decompensation or cumulative neurological impairment. Given the lack of therapeutic options for MSUD patients, we sought to develop an oral enzyme therapy that can degrade leucine within the gastrointestinal tract prior to its systemic absorption and thus enable patients to maintain acceptable plasma leucine levels while broadening their access to natural protein. We identified a highly active leucine decarboxylase enzyme from Planctomycetaceae bacterium and used directed evolution to engineer the enzyme for stability to gastric and intestinal conditions. Following high-throughput screening of over 12 000 enzyme variants over 9 iterative rounds of evolution, we identified a lead variant, LDCv10, which retains activity following simulated gastric or intestinal conditions in vitro. In intermediate MSUD mice or healthy nonhuman primates given a whey protein meal, oral treatment with LDCv10 suppressed the spike in plasma leucine and KIC and reduced the leucine area under the curve in a dose-dependent manner. Reduction in plasma leucine correlated with decreased brain leucine levels following oral LDCv10 treatment. Collectively, these data support further development of LDCv10 as a potential new therapy for MSUD patients.

Do Reactive Oxygen and Nitrogen Species Have a Similar Effect on Digestive Processes in Carnivorous Nepenthes Plants and Humans?

Carnivorous plants attract animals, trap and kill them, and absorb nutrients from the digested bodies. This unusual (for autotrophs) type of nutrient acquisition evolved through the conversion of photosynthetically active leaves into specialised organs commonly called traps. The genus Nepenthes (pitcher plants) consists of approximately 169 species belonging to the group of carnivorous plants. Pitcher plants are characterised by specialised passive traps filled with a digestive fluid. The digestion that occurs inside the traps of carnivorous plants depends on the activities of many enzymes. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) also participate in the digestive process, but their action is poorly recognised. ROS and RNS, named together as RONS, exhibit concentration-dependent bimodal functions (toxic or signalling). They act as antimicrobial agents, participate in protein modification, and are components of signal transduction cascades. In the human stomach, ROS are considered as the cause of different diseases. RNS have multifaceted functions in the gastrointestinal tract, with both positive and negative impacts on digestion. This review describes the documented and potential impacts of RONS on the digestion in pitcher plant traps, which may be considered as an external stomach.

Investigation of the oral microbiome of children associated with dental caries: A systematic study

OBJECTIVE

The present study aims to investigate the variations in dental caries (DC) related microbiome abnormality and metabolomics shift in children.

DESIGN

The patients were divided into two groups healthy control (C) and highly affected DC children based on inclusion and exclusion criteria. Saliva samples were collected and used for the taxonomic and functional characterization of oral microbiota.

RESULTS

Metatranscriptomics analysis revealed the alterations and composition of oral microbiota in the C and DC groups. Relative abundance in the C group was associated with Firmicutes, Actinobacteria, and Bacteroidetes. Whereas, the microbial composition in the DC group was found to be considerably altered with increases in the abundance of the Proteobacteria (25%), Fusobacteria (15%), and Cyanobacteria (8%) while decreases in the abundance of Firmicutes (10%) and Bacteroidetes (23%). Alterations in the phylum composition were positively and negatively correlated with several metabolites of sugars (such as fructose, sorbose, ribose, allose, and mannose) and amino acids (such as arginine, lysine, tryptophan, and proline). Moreover, in comparison with the C group, the metabolic shift of the DC group was different with an increase in certain tricarboxylic acid cycle intermediates levels, and a decrease in fatty acid. Such alterations can enhance the growth of oral pathogens and contribute to DC development.

CONCLUSIONS

The findings of this study suggest that an altered abundance of Actinobacillus, Fusobacterium, and Shuttleworthia can serve as biomarkers of DC in children.

Probiotic properties of Bacillus subtilis DG101 isolated from the traditional Japanese fermented food nattō

Spore-forming probiotic bacteria offer interesting properties as they have an intrinsic high stability, and when consumed, they are able to survive the adverse conditions encountered during the transit thorough the host gastrointestinal (GI) tract. A traditional healthy food, nattō, exists in Japan consisting of soy fermented by the spore-forming bacterium Bacillus subtilis natto. The consumption of nattō is linked to many beneficial health effects, including the prevention of high blood pressure, osteoporosis, and cardiovascular-associated disease. We hypothesize that the bacterium B. subtilis natto plays a key role in the beneficial effects of nattō for humans. Here, we present the isolation of B. subtilis DG101 from nattō and its characterization as a novel spore-forming probiotic strain for human consumption. B. subtilis DG101 was non-hemolytic and showed high tolerance to lysozyme, low pH, bile salts, and a strong adherence ability to extracellular matrix proteins (i.e., fibronectin and collagen), demonstrating its potential application for competitive exclusion of pathogens. B. subtilis DG101 forms robust liquid and solid biofilms and expresses several extracellular enzymes with activity against food diet-associated macromolecules (i.e., proteins, lipids, and polysaccharides) that would be important to improve food diet digestion by the host. B. subtilis DG101 was able to grow in the presence of toxic metals (i.e., chromium, cadmium, and arsenic) and decreased their bioavailability, a feature that points to this probiotic as an interesting agent for bioremediation in cases of food and water poisoning with metals. In addition, B. subtilis DG101 was sensitive to antibiotics commonly used to treat infections in medical settings, and at the same time, it showed a potent antimicrobial effect against pathogenic bacteria and fungi. In mammalians (i.e., rats), B. subtilis DG101 colonized the GI tract, and improved the lipid and protein serum homeostasis of animals fed on the base of a normal- or a deficient-diet regime (dietary restriction). In the animal model for longevity studies, Caenorhabditis elegans, B. subtilis DG101 significantly increased the animal lifespan and prevented its age-related behavioral decay. Overall, these results demonstrate that B. subtilis DG101 is the key component of nattō with interesting probiotic properties to improve and protect human health.

Decoding viruses: An alternative perspective on their history, origins and role in nature

This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.

Gastrointestinal Delivery of an mRNA Vaccine Using Immunostimulatory Polymeric Nanoparticles

mRNA vaccines can be translated into protein antigens, in vivo, to effectively induce humoral and cellular immunity against these proteins. While current mRNA vaccines have generated potent immune responses, the need for ultracold storage conditions (- 80 °C) and healthcare professionals to administer the vaccine through the parenteral route has somewhat limited their distribution in rural areas and developing countries. Overcoming these challenges stands to transform future deployment of mRNA vaccines. In this study, we developed an mRNA vaccine that can trigger a systemic immune response through administration via the gastrointestinal (GI) tract and is stable at 4 °C. A library of cationic branched poly(β-amino ester) (PBAE) polymers was synthesized and characterized, from which a polymer with high intracellular mRNA delivery efficiency and immune stimulation capacity was down-selected. mRNA vaccines made with the lead polymer-elicited cellular and humoral immunity in mice. Furthermore, lyophilization conditions of the formulation were optimized to enable storage under refrigeration. Our results suggest that PBAE nanoparticles are potent mRNA delivery platforms that can elicit B cell and T cell activation, including antigen-specific cellular and humoral responses. This system can serve as an easily administrable, potent oral mRNA vaccine.

A Critical Review on the Dosing and Safety of Antifungals Used in Exotic Avian and Reptile Species

Antifungals are used in exotic avian and reptile species for the treatment of fungal diseases. Dose extrapolations across species are common due to lack of species-specific pharmacological data. This may not be ideal because interspecies physiological differences may result in subtherapeutic dosing or toxicity. This critical review aims to collate existing pharmacological data to identify antifungals with the most evidence to support their safe and effective use. In the process, significant trends and gaps are also identified and discussed. An extensive search was conducted on PubMed and JSTOR, and relevant data were critically appraised. Itraconazole or voriconazole showed promising results in Japanese quails, racing pigeons and inland bearded dragons for the treatment of aspergillosis and CANV-related infections. Voriconazole neurotoxicity manifested as seizures in multiple penguins, but as lethargy or torticollis in cottonmouths. Itraconazole toxicity was predominantly hepatotoxicity, observed as liver abnormalities in inland bearded dragons and a Parson's chameleon. Differences in formulations of itraconazole affected various absorption parameters. Non-linearities in voriconazole due to saturable metabolism and autoinduction showed opposing effects on clearance, especially in multiple-dosing regimens. These differences in pharmacokinetic parameters across species resulted in varying elimination half-lives. Terbinafine has been used in dermatomycoses, especially in reptiles, due to its keratinophilic nature, and no significant adverse events were observed. The use of fluconazole has declined due to resistance or its narrow spectrum of activity.

The role of gastric microecological dysbiosis in gastric carcinogenesis

Gastric cancer (GC) is the leading cause of cancer-related death worldwide, and reducing its mortality has become an urgent public health issue. Gastric microecological dysbiosis (including bacteria, fungi, viruses, acid suppressants, antibiotics, and surgery) can lead to gastric immune dysfunction or result in a decrease in dominant bacteria and an increase in the number and virulence of pathogenic microorganisms, which in turn promotes development of GC. This review analyzes the relationship between gastric microecological dysbiosis and GC, elucidates dynamic alterations of the microbiota in Correa's cascade, and identifies certain specific microorganisms as potential biomarkers of GC to aid in early screening and diagnosis. In addition, this paper presents the potential of gastric microbiota transplantation as a therapeutic target for gastric cancer, providing a new direction for future research in this field.

Milk Transmission of Mammalian Retroviruses

The transmission of viruses from one host to another typically occurs through horizontal or vertical pathways. The horizontal pathways include transmission amongst individuals, usually through bodily fluids or excretions, while vertical transmission transpires from mother to their offspring, either during pregnancy, childbirth, or breastfeeding. While there are more than 200 human pathogenic viruses to date, only a small number of them are known to be transmitted via breast milk, including cytomegalovirus (CMV), human immunodeficiency virus type 1 (HIV-1), and human T cell lymphotropic virus type 1 (HTLV-1), the latter two belonging to the family Retroviridae. Breast milk transmission is a common characteristic among mammalian retroviruses, but there is a lack of reports summarizing our knowledge regarding this route of transmission of mammalian retroviruses. Here, we provide an overview of the transmission of mammalian exogenous retroviruses with a focus on Orthoretrovirinae, and we highlight whether they have been described or suspected to be transmitted through breast milk, covering various species. We also elaborate on the production and composition of breast milk and discuss potential entry sites of exogenous mammalian retroviruses during oral transmission.

Evolutionary implications of host genetic control for engineering beneficial microbiomes

Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.

Effects of dietary irritants on intestinal homeostasis and the intervention strategies

Abundant diet components are unexplored as vital factors in intestinal homeostasis. Dietary irritants stimulate the nervous system and provoke somatosensory responses, further inducing diarrhea, gut microbiota disorder, intestinal barrier damage or even severe gastrointestinal disease. We depicted the effects of food with piquancy, high fat, low pH, high-refined carbohydrates, and indigestible texture. The mechanism of dietary irritants on intestinal homeostasis were comprehensively summarized. Somatosensory responses to dietary irritants are palpable and have specific chemical and neural mechanisms. In contrast, even low-dose exposure to dietary irritants can involve multiple intestinal barriers. Their mechanisms in intestinal homeostasis are often overlapping and dose-dependent. Therefore, treating symptoms caused by dietary irritants requires personalized nutritional advice. The reprocessing of stimulant foods, additional supplementation with probiotics or prebiotics, and enhancement of the intestinal barrier are effective intervention strategies. This review provides promising preliminary guidelines for the treatment of symptoms and gastrointestinal injury caused by dietary irritants.

Characterization and evaluation of the cholesterol-lowering ability of Lactiplantibacillus plantarum HJ-S2 isolated from the intestine of Mesoplodon densirostris

In this study, ten strains of lactic acid bacteria were isolated from the intestine of Blainville's beaked whale (Mesoplodon densirostris),and their cholesterol-lowering activities in vitro and in vivo were investigated. The among these strains, HJ-S2 strain, which identified as Lactiplantibacillus plantarum, showed a high in vitro cholesterol-lowering rate (48.82%). Strain HJ-S2 was resistant to acid and bile salts, with a gastrointestinal survival rate of more than 80%, but was sensitive to antibiotics. Strain HJ-S2 was found to be able to adhere to HT-29 cells in an adhesion test. The number of cell adhesion was 132.52. In addition, we also performed the cholesterol-lowering activities in vivo using high-fat diet feed mouse models. Our results indicated that HJ-S2 reduced total cholesterol (TC), total glycerol (TG), and low-density lipoprotein cholesterol (LDLC) levels while increasing the high-density lipoprotein cholesterol (HDLC) level. It also alleviated the lipid accumulation in high-fat diet feed mouse liver and pancreas. Hence, HJ-S2 demonstrated appropriate cholesterol-lowering ability and has the potential to be used as a probiotic in functional foods.

Bacterial chemotaxis in human diseases

To infect and cause disease, bacterial pathogens must localize to specific regions of the host where they possess the metabolic and defensive acumen for survival. Motile flagellated pathogens exercise control over their localization through chemotaxis to direct motility based on the landscape of exogenous nutrients, toxins, and molecular cues sensed within the host. Here, we review advances in understanding the roles chemotaxis plays in human diseases. Chemotaxis drives pathogen colonization to sites of inflammation and injury and mediates fitness advantages through accessing host-derived nutrients from damaged tissue. Injury tropism may worsen clinical outcomes through instigating chronic inflammation and subsequent cancer development. Inhibiting bacterial chemotactic systems could act synergistically with antibacterial medicines for more effective and specific eradication.

Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs

Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.

Understanding and mitigating thiaminase activity in silver carp

A deficiency of thiamine (vitamin B1), an essential cofactor for enzymes involved in metabolic processes, can be caused by the enzyme thiaminase. Thiaminase in food stocks has been linked to morbidity and mortality due to thiamine depletion in many ecologically and economically important species. Thiaminase activity has been detected in certain bacteria, plants, and fish species, including carp. The invasive silver carp (Hypophthalmichthys molitrix) presents an enormous burden to ecosystems throughout the Mississippi River watershed. Its large biomass and nutritional content offer an attractive possibility as a food source for humans, wild animals, or pets. Additionally, harvesting this fish could alleviate some of the effects of this species on waterways. However, the presence of thiaminase would detract from its value for dietary consumption. Here we confirm the presence of thiaminase in several tissues from silver carp, most notably the viscera, and systematically examine the effects of microwaving, baking, dehydrating, and freeze-drying on thiaminase activity. Certain temperatures and durations of baking and microwaving reduced thiaminase activity to undetectable levels. However, caution should be taken when carp tissue is concentrated by processes without sufficient heat treatment, such as freeze-drying or dehydration, which results in concentration, but not inactivation of the enzyme. The effects of such treatments on the ease of extracting proteins, including thiaminase, and the impact on data interpretation using the 4-nitrothiophenol (4-NTP) thiaminase assay were considered.