Effects of Antibiotics upon the Gut Microbiome: A Review of the Literature

High sugar diet alters immune function and the gut microbiome in juvenile green iguanas (Iguana iguana)

The present work aimed to study whether a high sugar diet can alter immune responses and the gut microbiome in green iguanas. Thirty-six iguanas were split into four treatment groups using a 2×2 design. Iguanas received either a sugar-supplemented diet or a control diet, and either a lipopolysaccharide (LPS) injection or a phosphate-buffered saline (PBS) injection. Iguanas were given their respective diet treatment through the entire study (∼3 months) and received a primary immune challenge 1 and 2 months into the experiment. Blood samples and cloacal swabs were taken at various points in the experiment and used to measure changes in the immune system (bacterial killing ability, lysis and agglutination scores, LPS-specific IgY concentrations), and alterations in the gut microbiome. We found that a sugar diet reduces bacterial killing ability following an LPS challenge, and sugar and the immune challenge temporarily alters gut microbiome composition while reducing alpha diversity. Although sugar did not directly reduce lysis and agglutination following the immune challenge, the change in these scores over a 24-h period following an immune challenge was more drastic (it decreased) relative to the control diet group. Moreover, sugar increased constitutive agglutination outside of the immune challenges (i.e. pre-challenge levels). In this study, we provide evidence that a high sugar diet affects the immune system of green iguanas (in a disruptive manner) and alters the gut microbiome.

Nisin Inhibition of Gram-Negative Bacteria

Aims: This study investigates the activity of the broad-spectrum bacteriocin nisin against a large panel of Gram-negative bacterial isolates, including relevant plant, animal, and human pathogens. The aim is to generate supportive evidence towards the use/inclusion of bacteriocin-based therapeutics and open avenues for their continued development. Methods and Results: Nisin inhibitory activity was screened against a panel of 575 strains of Gram-negative bacteria, encompassing 17 genera. Nisin inhibition was observed in 309 out of 575 strains, challenging the prevailing belief that nisin lacks effectiveness against Gram-negative bacteria. The genera Acinetobacter, Helicobacter, Erwinia, and Xanthomonas exhibited particularly high nisin sensitivity. Conclusions: The findings of this study highlight the promising potential of nisin as a therapeutic agent for several key Gram-negative plant, animal, and human pathogens. These results challenge the prevailing notion that nisin is less effective or ineffective against Gram-negative pathogens when compared to Gram-positive pathogens and support future pursuits of nisin as a complementary therapy to existing antibiotics. Significance and Impact of Study: This research supports further exploration of nisin as a promising therapeutic agent for numerous human, animal, and plant health applications, offering a complementary tool for infection control in the face of multidrug-resistant bacteria.

Expert consensus-based clinical recommendation for an integrative anthroposophic treatment approach to acute tonsillitis in childhood

BACKGROUND

Medical guidelines are an important basis for qualitative and cost-effective patient care. However, there is a lack of clinical recommendations in anthroposophic medicine (AM), an integrative medicine approach frequently practised in Europe. Acute tonsillitis, which includes tonsillopharyngitis, is a common childhood disease. that is mostly caused by a viral infection. Symptomatic treatment is therefore of high importance, and AM can offer several therapy options.

METHODS

53 physicians from Germany, Spain, Netherlands, Switzerland, Austria, and Hungary with at least one year of experience in anthroposophic paediatric medicine were invited to participate in an online Delphi process. The process comprises five survey rounds starting with open-ended questions and ending with final statements, which need 75% agreement of experts to reach consensus. Expert answers were evaluated by two independent reviewers using MAXQDA and Excel.

RESULTS

Response rate was between 28% and 45%. The developed recommendation included 15 subtopics. These covered clinical, diagnostic, therapeutic and psychosocial aspects of acute tonsillitis. Six subtopics achieved a high consensus (>90%) and nine subtopics achieved consensus (75-90%).

CONCLUSION

The clinical recommendation for acute tonsillitis in children aims to simplify everyday patient care and provide decision-making support when considering and prescribing anthroposophic therapies. Moreover, the recommendation makes AM more transparent for physicians, parents, and maybe political stakeholders as well.

The Profound Influence of Gut Microbiome and Extracellular Vesicles on Animal Health and Disease

The animal gut microbiota, comprising a diverse array of microorganisms, plays a pivotal role in shaping host health and physiology. This review explores the intricate dynamics of the gut microbiome in animals, focusing on its composition, function, and impact on host-microbe interactions. The composition of the intestinal microbiota in animals is influenced by the host ecology, including factors such as temperature, pH, oxygen levels, and nutrient availability, as well as genetic makeup, diet, habitat, stressors, and husbandry practices. Dysbiosis can lead to various gastrointestinal and immune-related issues in animals, impacting overall health and productivity. Extracellular vesicles (EVs), particularly exosomes derived from gut microbiota, play a crucial role in intercellular communication, influencing host health by transporting bioactive molecules across barriers like the intestinal and brain barriers. Dysregulation of the gut-brain axis has implications for various disorders in animals, highlighting the potential role of microbiota-derived EVs in disease progression. Therapeutic approaches to modulate gut microbiota, such as probiotics, prebiotics, microbial transplants, and phage therapy, offer promising strategies for enhancing animal health and performance. Studies investigating the effects of phage therapy on gut microbiota composition have shown promising results, with potential implications for improving animal health and food safety in poultry production systems. Understanding the complex interactions between host ecology, gut microbiota, and EVs provides valuable insights into the mechanisms underlying host-microbe interactions and their impact on animal health and productivity. Further research in this field is essential for developing effective therapeutic interventions and management strategies to promote gut health and overall well-being in animals.

Gut microbiota in relationship to diabetes mellitus and its late complications with a focus on diabetic foot syndrome: A review

Diabetes mellitus is a chronic disease affecting glucose metabolism. The pathophysiological reactions underpinning the disease can lead to the development of late diabetes complications. The gut microbiota plays important roles in weight regulation and the maintenance of a healthy digestive system. Obesity, diabetes mellitus, diabetic retinopathy, diabetic nephropathy and diabetic neuropathy are all associated with a microbial imbalance in the gut. Modern technical equipment and advanced diagnostic procedures, including xmolecular methods, are commonly used to detect both quantitative and qualitative changes in the gut microbiota. This review summarises collective knowledge on the role of the gut microbiota in both types of diabetes mellitus and their late complications, with a particular focus on diabetic foot syndrome.

Utilization of broad- versus narrow-spectrum antibiotics for the treatment of outpatient community-acquired pneumonia among adults in the United States

PURPOSE

To characterize antibiotic utilization for outpatient community-acquired pneumonia (CAP) in the United States.

METHODS

We conducted a cohort study among adults 18-64 years diagnosed with outpatient CAP and a same-day guideline-recommended oral antibiotic fill in the MarketScan® Commercial Database (2008-2019). We excluded patients coded for chronic lung disease or immunosuppressive disease; recent hospitalization or frequent healthcare exposure (e.g., home wound care, patients with cancer); recent antibiotics; or recent infection. We characterized utilization of broad-spectrum antibiotics (respiratory fluoroquinolone, β-lactam + macrolide, β-lactam + doxycycline) versus narrow-spectrum antibiotics (macrolide, doxycycline) overall and by patient- and provider-level characteristics. Per 2007 IDSA/ATS guidelines, we stratified analyses by otherwise healthy patients and patients with comorbidities (coded for diabetes; chronic heart, liver, or renal disease; etc.).

RESULTS

Among 263 914 otherwise healthy CAP patients, 35% received broad-spectrum antibiotics (not recommended); among 37 161 CAP patients with comorbidities, 44% received broad-spectrum antibiotics (recommended). Ten-day antibiotic treatment durations were the most common for all antibiotic classes except macrolides. From 2008 to 2019, broad-spectrum antibiotic use substantially decreased from 45% to 19% in otherwise healthy patients (average annual percentage change [AAPC], -7.5% [95% CI -9.2%, -5.9%]), and from 55% to 29% in patients with comorbidities (AAPC, -5.8% [95% CI -8.8%, -2.6%]). In subgroup analyses, broad-spectrum antibiotic use varied by age, geographic region, provider specialty, and provider location.

CONCLUSIONS

Real-world use of broad-spectrum antibiotics for outpatient CAP declined over time but remained common, irrespective of comorbidity status. Prolonged duration of therapy was common. Antimicrobial stewardship is needed to aid selection according to comorbidity status and to promote shorter courses.

Can the Evidence-Based Use of Probiotics (Notably Saccharomyces boulardii CNCM I-745 and Lactobacillus rhamnosus GG) Mitigate the Clinical Effects of Antibiotic-Associated Dysbiosis?

Dysbiosis corresponds to the disruption of a formerly stable, functionally complete microbiota. In the gut, this imbalance can lead to adverse health outcomes in both the short and long terms, with a potential increase in the lifetime risks of various noncommunicable diseases and disorders such as atopy (like asthma), inflammatory bowel disease, neurological disorders, and even behavioural and psychological disorders. Although antibiotics are highly effective in reducing morbidity and mortality in infectious diseases, antibiotic-associated diarrhoea is a common, non-negligible clinical sign of gut dysbiosis (and the only visible one). Re-establishment of a normal (functional) gut microbiota is promoted by completion of the clinically indicated course of antibiotics, the removal of any other perturbing external factors, the passage of time (i.e. recovery through the microbiota's natural resilience), appropriate nutritional support, and-in selected cases-the addition of probiotics. Systematic reviews and meta-analyses of clinical trials have confirmed the strain-specific efficacy of some probiotics (notably the yeast Saccharomyces boulardii CNCM I-745 and the bacterium Lactobacillus rhamnosus GG) in the treatment and/or prevention of antibiotic-associated diarrhoea in children and in adults. Unusually for a probiotic, S. boulardii is a eukaryote and is not therefore directly affected by antibiotics-making it suitable for administration in cases of antibiotic-associated diarrhoea. A robust body of evidence from clinical trials and meta-analyses shows that the timely administration of an adequately dosed probiotic (upon initiation of antibiotic treatment or within 48 h) can help to prevent or resolve the consequences of antibiotic-associated dysbiosis (such as diarrhoea) and promote the resilience of the gut microbiota and a return to the pre-antibiotic state. A focus on the prescription of evidence-based, adequately dosed probiotics should help to limit unjustified and potentially ineffective self-medication.

Cardiovascular diseases and the heart-gut cross talk

The purpose of this narrative review is to provide a comprehensive overview of current research on heart-gut cross talk and its implications for cardiovascular disease. To uncover relevant preclinical and clinical research examining heart-gut cross talk, a thorough literature search was undertaken utilising electronic databases. The chosen publications were critically examined, and major findings were synthesised to offer a thorough perspective on the subject. We want to synthesise the most recent study findings, explain the underlying mechanisms, and provide potential treatment techniques. By exploring bidirectional connection between the heart and the gut, we shed light on novel future options for the prevention and treatment of cardiovascular diseases. The heart-gut cross talk is an exciting field of study with implications for cardiovascular disease. Understanding the complex connection between the heart and the gastrointestinal tract may lead to the development of novel therapeutic targets and therapies for the prevention and management of cardiovascular diseases. Future research should concentrate on identifying the specific processes driving this crosstalk as well as assessing the efficacy of therapies targeting the gut microbiota and the gut-brain axis in improving cardiovascular outcomes.

Challenges in the profitability of small-scale broiler farming by avoiding injudicious use of drugs and additives

The aim of the current study was to determine the present scenario of injudicious use of drugs and additives in small-scale broiler operations and whether broilers can be produced successfully and profitably without the injudicious use of drugs and additives. First, a survey was undertaken in relation to farmers' basic information and general management methods in commercial broilers, with special attention given to the usage of medications and additives in drinking water. Second, based on the survey data, an experimental trial was carried out to compare the growth performance and economic profitability of rearing broilers with and without the use of said drugs and additives. A total of 540 broiler DOCs were allotted into three treatments: T1 = self-formulated feed (SFF) with judicious use of drugs and additives; T2 = commercial feed with judicious use of drugs and additives (JUDA) and T3 = commercial feed with injudicious use of drugs and additives (InJUDA), with six replications (30 birds/replication) in each. The results showed that the farmers used a variety of drugs and additives in 35 days of broiler rearing; however, the farmers usually did not consult with veterinary practitioners, instead relying on and being instructed by local dealers and medicine company representatives. Although the medications and additives account for almost 6-8% of total production costs, the experimental trial clearly demonstrated that the broilers kept with either JUDA or InJUDA showed statistically (p < 0.05) similar BW (2181.93 g & 2222.53 g/bird), BWG (2110.0 g & 2129.91 g/bird), and FCR (1.62 & 1.57, respectively), whereas broilers in the SFF group showed significantly lower growth performances (BW = 1799.31 g/bird, BWG = 1746.19 g/bird, and FCR = 1.93, respectively). The net profit per kg bird in the JUDA group was substantially (p < 0.05) greater (BDT- 27.34/-), followed by the SFF group (BDT- 25.56/) and the InJUDA group (BDT- 24.49/-). Taken together, these findings suggest that profitable broiler farming is possible without the injudicious use of drugs and additives.

Standardization of the protocol for oral cavity examination and collecting of the biological samples for microbiome research using the next-generation sequencing (NGS): own experience with the COVID-19 patients

To date, publications have shown that compositions of oral microbiota differ depending on their habitats (e.g. tongue, tonsils, pharynx). The absence of set standards for the choice of the areas and conditions of material collection makes the oral microbiome one of the most difficult environments for a comparative analysis with other researchers, which is a meaningful limitation during an assessment of the potential effects of microorganisms as biomarkers in the courses of various human diseases. Therefore, standardisation of basic conditions of a dental examination and collection of material for the next generation sequencing (NGS) is worth attempting. The standardisation of the dental exam and collection of the clinical materials: saliva, swab from the tongue ridge, hard palate, palatine tonsils and oropharynx, supragingival plaque and subgingival plaque. Protocol involved the patients (n = 60), assigned to 3 groups: I-COVID-19 convalescents who received antibiotics, n = 17, II-COVID-19 convalescents, n = 23 and III-healthy individuals, n = 20. The collected biological samples were used to conduct NGS (16S rRNA). The conditions of patient preparation for collecting biological materials as well as the schedule of dental examination, were proposed. Based on the research conducted, we have indicated the dental indicators that best differentiate the group of COVID-19 patients (groups I and II) from healthy people (group III). These include the DMFT, D and BOP indices. The use of alpha and beta diversity analysis provided an overall insight into the diversity of microbial communities between specific niches and patient groups. The most different diversity between the studied group of patients (group II) and healthy people (group III) was noted in relation to the supragingival plaque. The order of activities during the dental exam as well as while collecting and securing clinical materials is particularly important to avoid technical errors and material contamination which may result in erroneous conclusions from the analyses of the results of sensitive tests such as the NGS. It has been shown that the dental indices: DMFT, D number, PI and BOP are the best prognostic parameters to assess the oral health. Based on beta diversity the most sensitive niche and susceptible to changes in the composition of the microbiota is the supragingival plaque. The procedures developed by our team can be applied as ready-to-use forms in studies conducted by other researchers.

Could Adverse Effects of Antibiotics Due to Their Use/Misuse Be Linked to Some Mechanisms Related to Nonalcoholic Fatty Liver Disease?

Nonalcoholic fatty liver disease, recently re-named metabolic dysfunction-associated steatotic fatty liver disease, is considered the most prevalent liver disease worldwide. Its molecular initiation events are multiple and not always well-defined, comprising insulin resistance, chronic low-grade inflammation, gut dysbiosis, and mitochondrial dysfunction, all of them acting on genetic and epigenetic grounds. Nowadays, there is a growing public health threat, which is antibiotic excessive use and misuse. This widespread use of antibiotics not only in humans, but also in animals has led to the presence of residues in derived foods, such as milk and dairy products. Furthermore, antibiotics have been used for many decades to control certain bacterial diseases in high-value fruit and vegetables. Recently, it has been emphasised that antibiotic-induced changes in microbial composition reduce microbial diversity and alter the functional attributes of the microbiota. These antibiotic residues impact human gut flora, setting in motion a chain of events that leads straight to various metabolic alterations that can ultimately contribute to the onset and progression of NAFLD.

The Role of the Gut Microbiome and Microbial Dysbiosis in Common Skin Diseases

Dermatoses are an increasingly common problem, particularly in developed countries. The causes of this phenomenon include genetic factors and environmental elements. More and more scientific reports suggest that the gut microbiome, more specifically its dysbiosis, also plays an important role in the induction and progression of diseases, including dermatological diseases. The gut microbiome is recognised as the largest endocrine organ, and has a key function in maintaining human homeostasis. In this review, the authors will take a close look at the link between the gut-skin axis and the pathogenesis of dermatoses such as atopic dermatitis, psoriasis, alopecia areata, and acne. The authors will also focus on the role of probiotics in remodelling the microbiome and the alleviation of dermatoses.

Decoding the role of the gut microbiome in gut-brain axis, stress-resilience, or stress-susceptibility: A review

Increased exposure to stress is associated with stress-related disorders, including depression, anxiety, and neurodegenerative conditions. However, susceptibility to stress is not seen in every individual exposed to stress, and many of them exhibit resilience. Thus, developing resilience to stress could be a big breakthrough in stress-related disorders, with the potential to replace or act as an alternative to the available therapies. In this article, we have focused on the recent advancements in gut microbiome research and the potential role of the gut-brain axis (GBA) in developing resilience or susceptibility to stress. There might be a complex interaction between the autonomic nervous system (ANS), immune system, endocrine system, microbial metabolites, and bioactive lipids like short-chain fatty acids (SCFAs), neurotransmitters, and their metabolites that regulates the communication between the gut microbiota and the brain. High fiber intake, prebiotics, probiotics, plant supplements, and fecal microbiome transplant (FMT) could be beneficial against gut dysbiosis-associated brain disorders. These could promote the growth of SCFA-producing bacteria, thereby enhancing the gut barrier and reducing the gut inflammatory response, increase the expression of the claudin-2 protein associated with the gut barrier, and maintain the blood-brain barrier integrity by promoting the expression of tight junction proteins such as claudin-5. Their neuroprotective effects might also be related to enhancing the expression of brain-derived neurotrophic factor (BDNF) and glucagon-like peptide (GLP-1). Further investigations are needed in the field of the gut microbiome for the elucidation of the mechanisms by which gut dysbiosis contributes to the pathophysiology of neuropsychiatric disorders.

Pushing the frontiers in the fight against antimicrobial resistance: the potential of fecal and maggot therapies

The escalating crisis of antimicrobial resistance (AMR) warrants innovative therapeutic strategies. Fecal microbiota transplantation (FMT) and maggot debridement therapy (MDT) represent paradigm-shifting approaches, leveraging biological systems to mitigate AMR. FMT restores a healthy gut microbiome, providing a biotherapeutic counter to pathogenic bacteria, thereby reducing reliance on traditional antibiotics. Conversely, MDT, a form of bio-debridement, utilizes the antimicrobial secretions of maggots to cleanse wounds and eliminate resistant bacteria. Despite the promise these therapies hold, their broader clinical adoption faces multifaceted challenges including the need for rigorous scientific substantiation, standardized protocols, deepened understanding of mechanisms of action, and surmounting regulatory and public acceptance barriers. However, their potential integration with precision medicine could revolutionize disease management, particularly with antibiotic-resistant infections.

Oral microbiota study of the patients after hospitalisation for COVID-19, considering selected dental indices and antibiotic therapy using the next generation sequencing method (NGS)

Background

Poor oral hygiene and the increased incidence and severity of periodontitis may exacerbate SARS-CoV-2 infection. The aim was to evaluate the oral microbiota of 60 participants divided into groups: COVID-19 convalescents who received antibiotics during hospitalization (I), COVID-19 convalescents without antibiotic therapy (II) and healthy individuals (III).

Materials and Methods

Dental examination was conducted, and oral health status was evaluated using selected dental indexes. Clinical samples (saliva, dorsal swabs, supragingival and subgingival plaque) were collected and used for metagenomic library to the next-generation sequencing (NGS) preparation.

Results

Each of the clinical materials in particular groups of patients showed a statistically significant and quantitatively different bacterial composition. Patients from group I showed significantly worse oral health, reflected by higher average values of dental indexes and also a higher percentage of Veillonella, Tannerella, Capnocytophaga and Selenomonas genera in comparison to other groups. Additionally, a statistically significant decrease in the amount of Akkermansia type in both groups with COVID-19 was observed for all materials.

Conclusions

The primary factor affecting the composition of oral microbiota was not the SARS-CoV-2 infection itself, but the use of antibiotic therapy. The increased percentage of pro-inflammatory pathogens observed in COVID-19 patients underscores the importance of preventing periodontal disease and improving oral hygiene in the future.

The gut microbiome and cardiac surgery an unusual symphony

The relationship between the gut microbiome and various organ systems has gained interest throughout the scientific community in recent times. The understanding of these complex relationships has greatly improved with clinical benefits now being seen. Cardiopulmonary bypass (CPB) is a form of extracorporeal circulation that provides circulatory and respiratory support during cardiac surgery. This physiological support facilitates a still and bloodless field facilitating operations on the heart to be performed. Through various mechanisms CPB results in a systemic inflammatory response syndrome (SIRS). This response can vary from mild hypotension to multiple organ failure. It remains difficult to predict the degree to which a patient will experience SIRS post-operatively. The relationship between the composition of the gut microbiome and inflammatory processes associated with disease has been seen across several fields including gastroenterology, neurology, psychiatry and cardiology. To date, minimal research has been undertaken to examine the impact the gut microbiome has on outcomes following cardiac surgery. This review paper explores the pathophysiology behind the SIRS response associated with CPB for cardiac surgery and the hypothesis that a correlation exists between a patients gut microbiome composition and the degree of inflammatory response experienced following cardiac surgery.

Elucidating the roles of the mammary and gut microbiomes in breast cancer development

The mammary microbiome is a newly characterized bacterial niche that might offer biological insight into the development of breast cancer. Together with in-depth analysis of the gut microbiome in breast cancer, current evidence using next-generation sequencing and metabolic profiling suggests compositional and functional shifts in microbial consortia are associated with breast cancer. In this review, we discuss the fundamental studies that have progressed this important area of research, focusing on the roles of both the mammary tissue microbiome and the gut microbiome. From the literature, we identified the following major conclusions, (I) There are unique breast and gut microbial signatures (both compositional and functional) that are associated with breast cancer, (II) breast and gut microbiome compositional and breast functional dysbiosis represent potential early events of breast tumor development, (III) specific breast and gut microbes confer host immune responses that can combat breast tumor development and progression, and (IV) chemotherapies alter the microbiome and thus maintenance of a eubiotic microbiome may be key in breast cancer treatment. As the field expectantly advances, it is necessary for the role of the microbiome to continue to be elucidated using multi-omic approaches and translational animal models in order to improve predictive, preventive, and therapeutic strategies for breast cancer.

Pre-traumatic antibiotic-induced microbial depletion reduces neuroinflammation in acute murine traumatic brain injury

The connection between dysbiosis of the gut microbiome and diseases and injuries of the brain has attracted considerable interest in recent years. Interestingly, antibiotic-induced microbial dysbiosis has been implicated in the pathogenesis of traumatic brain injury (TBI), while early administration of antibiotics associates with improved survival in TBI patients. In animal models of TBI, short- or long-term administration of antibiotics, both peri- or post-operatively, were shown to induce gut microbiome dysbiosis but also anti-inflammatory and neuroprotective effects. However, the acute consequences of microbial dysbiosis on TBI pathogenesis after discontinuation of antibiotic treatment are elusive. In this study, we tested whether pre-traumatic antibiotic-induced microbial depletion by vancomycin, amoxicillin, and clavulanic acid affects pathogenesis during the acute phase of TBI in adult male C57BL/6 mice. Pre-traumatic microbiome depletion did not affect neurological deficits over 72 h post injury (hpi) and brain histopathology, including numbers of activated astrocytes and microglia, at 72 hpi. However, astrocytes and microglia were smaller after pre-traumatic microbiome depletion compared to vehicle treatment at 72hpi, indicating less inflammatory activation. Accordingly, TBI-induced gene expression of the inflammation markers Interleukin-1β, complement component C3, translocator protein TSPO and the major histocompatibility complex MHC2 was attenuated in microbiome-depleted mice along with reduced Immunoglobulin G extravasation as a proxy of blood-brain barrier (BBB) impairment. These results suggest that the gut microbiome contributes to early neuroinflammatory responses to TBI but does not have a significant impact on brain histopathology and neurological deficits.

Prevalence, Pathogenic Bacterial Profile and Antimicrobial Susceptibility Pattern of Urinary Tract Infection Among Children with Congenital Anomalies of the Kidney and Urinary Tract

Purpose

The study was to detect the pathogenic bacterial profile and antibiogram among children with congenital anomalies of the kidney and urinary tract (CAKUT).

Patients and Methods

A retrospective analysis was performed using medical records of urine culture results and antibiotic susceptibility results in patients with UTIs from March 2017 to March 2022. Antimicrobial susceptibility pattern was determined by a standard agar disc diffusion method.

Results

A total of 568 children were included. The proportion of culture-positive UTI was 59.15% (336/568). More than nine types of bacteria were isolated with most pathogens being Gram-negative species. Among Gram-negative isolates, the predominant bacteria were Escherichia coli (30.95%, 104/336) followed by Klebsiella pneumoniae (9.23%). Escherichia coli isolates were highly sensitive to amikacin (95.19%), ertapenem (94.23%), nitrofurantoin (93.27%), imipenem (91.35%), and piperacillin-tazobactam (90.38%) and high rate of resistant were also detected to ampicillin (92.31%), cephazolin (73.08%), ceftriaxone (70.19%), trimethoprim-sulfamethoxazole (61.54%) and ampicillin-sulbactam (57.69%). Klebsiella pneumoniae isolates showed sensitive to ertapenem (96.77%), amikacin (96.77%), imipenem (93.55%), piperacillin-tazobactam (90.32%) and gentamicin (83.87%), while highly resistant were observed to ampicillin (96.77%), cephazolin (74.19%), ceftazidime (61.29%), ceftriaxone (61.29%), and aztreonam (61.29%). The isolated Gram-positive bacteria mainly contained Enterococcus faecalis and Enterococcus faecium (each 15.77%). Enterococcus faecalis were sensitive to vancomycin, penicillin-G, tigecycline, nitrofurantoin and linezolid (100%, 94.34%, 88.68%, 88.68%, 86.79, respectively) and resistant to tetracycline (86.79%), quinupristi (83.02%), erythromycin (73.58%). Enterococcus faecium also showed a similar result. Multiple drug resistance (MDR) was observed in 264 (80.00%) of the 360 bacterial isolates. Only age was significantly associated with a culture-positive UTI.

Conclusion

A higher prevalence of culture-positive UTI was detected. Escherichia coli was the most prevalent uropathogen followed by Enterococcus faecalis and Enterococcus faecium. These uropathogens showed highly resistant to the commonly used antibiotics. Moreover, MDR was commonly observed. Thus, empiric therapy is unsatisfactory as drug sensitivity always varies over time.

Neurodegenerative and Neurodevelopmental Diseases and the Gut-Brain Axis: The Potential of Therapeutic Targeting of the Microbiome

The human gut microbiome contains the largest number of bacteria in the body and has the potential to greatly influence metabolism, not only locally but also systemically. There is an established link between a healthy, balanced, and diverse microbiome and overall health. When the gut microbiome becomes unbalanced (dysbiosis) through dietary changes, medication use, lifestyle choices, environmental factors, and ageing, this has a profound effect on our health and is linked to many diseases, including lifestyle diseases, metabolic diseases, inflammatory diseases, and neurological diseases. While this link in humans is largely an association of dysbiosis with disease, in animal models, a causative link can be demonstrated. The link between the gut and the brain is particularly important in maintaining brain health, with a strong association between dysbiosis in the gut and neurodegenerative and neurodevelopmental diseases. This link suggests not only that the gut microbiota composition can be used to make an early diagnosis of neurodegenerative and neurodevelopmental diseases but also that modifying the gut microbiome to influence the microbiome-gut-brain axis might present a therapeutic target for diseases that have proved intractable, with the aim of altering the trajectory of neurodegenerative and neurodevelopmental diseases such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, autism spectrum disorder, and attention-deficit hyperactivity disorder, among others. There is also a microbiome-gut-brain link to other potentially reversible neurological diseases, such as migraine, post-operative cognitive dysfunction, and long COVID, which might be considered models of therapy for neurodegenerative disease. The role of traditional methods in altering the microbiome, as well as newer, more novel treatments such as faecal microbiome transplants and photobiomodulation, are discussed.

Modulation of Gut Microbiota through Low-Calorie and Two-Phase Diets in Obese Individuals

Different nutritional regimens have been reported to exert beneficial effects on obesity through the regulation of the composition and function of gut microbiota. In this context, we conducted in obese subjects two dietary interventions consisting of a low-calorie and two-phase (ketogenic plus low-calorie) diet for 8 weeks. Anthropometric and clinical parameters were evaluated at baseline and following the two diets, and gut microbiota composition was assessed by 16S rRNA gene sequencing. A significant reduction was observed for abdominal circumference and insulin levels in the subjects following the two-phase diet. Significant differences in gut microbial composition were observed after treatment compared to the baseline. Both diets induced taxonomic shifts including a decrease in Proteobacteria, which are recognized as dysbiosis markers and enrichment of Verrucomicrobiaceae, which has recently emerged as an effective probiotic. An increase in Bacteroidetes, constituting the so-called good bacteria, was observable only in the two-phase diet. These findings provide evidence that a targeted nutritional regimen and an appropriate use of probiotics can modulate gut microbiota to reach a favorable composition and achieve the balance often compromised by different pathologies and conditions, such as obesity.

Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership

BACKGROUND

Many animals and plants acquire their coevolved symbiotic partners shortly post-embryonic development. Thus, during embryogenesis, cellular features must be developed that will promote both symbiont colonization of the appropriate tissues, as well as persistence at those sites. While variation in the degree of maturation occurs in newborn tissues, little is unknown about how this variation influences the establishment and persistence of host-microbe associations.

RESULTS

The binary symbiosis model, the squid-vibrio (Euprymna scolopes-Vibrio fischeri) system, offers a way to study how an environmental gram-negative bacterium establishes a beneficial, persistent, extracellular colonization of an animal host. Here, we show that bacterial symbionts occupy six different colonization sites in the light-emitting organ of the host that have both distinct morphologies and responses to antibiotic treatment. Vibrio fischeri was most resilient to antibiotic disturbance when contained within the smallest and least mature colonization sites. We show that this variability in crypt development at the time of hatching allows the immature sites to act as a symbiont reservoir that has the potential to reseed the more mature sites in the host organ when they have been cleared by antibiotic treatment. This strategy may produce an ecologically significant resiliency to the association.

CONCLUSIONS

The data presented here provide evidence that the evolution of the squid-vibrio association has been selected for a nascent organ with a range of host tissue maturity at the onset of symbiosis. The resulting variation in physical and chemical environments results in a spectrum of host-symbiont interactions, notably, variation in susceptibility to environmental disturbance. This "insurance policy" provides resiliency to the symbiosis during the critical period of its early development. While differences in tissue maturity at birth have been documented in other animals, such as along the infant gut tract of mammals, the impact of this variation on host-microbiome interactions has not been studied. Because a wide variety of symbiosis characters are highly conserved over animal evolution, studies of the squid-vibrio association have the promise of providing insights into basic strategies that ensure successful bacterial passage between hosts in horizontally transmitted symbioses. Video Abstract.

Microbial profiles and immune responses in seahorse gut and brood pouch under chronic exposure to environmental antibiotics

Ocean antibiotics pose substantial risks to the adaptation and lifespan of marine organisms. Seahorses are unique owing to the occurrence of brood pouches, male pregnancy, and loss of gut-associated lymphatic tissues and spleen, which lead to increased sensitivity to environmental changes. This study evaluated the changes in microbial diversity and immune responses within the gut and brood pouch in the lined seahorse Hippocampus erectus under chronic exposure to environmental levels of triclosan (TCS) and sulfamethoxazole (SMX), which are common antibiotics in coastal regions. The results showed that microbial abundance and diversity within the gut and brood pouch of seahorses were significantly changed following antibiotics treatment, with the expression of core genes involved in immunity, metabolism, and circadian rhythm processes evidently regulated. Notably, the abundance of potential pathogens in brood pouches was considerably increased upon treatment with SMX. Transcriptome analysis revealed that the expression of toll-like receptors, c-type lectins, and inflammatory cytokine genes in brood pouches was significantly upregulated. Notably, some essential genes related to male pregnancy significantly varied after antibiotic treatment, implying potential effects on seahorse reproduction. This study provides insights into the physiological adaptation of marine animals to environmental changes resulting from human activity.

The microbiota in feces of domestic pigeons in Seoul, Korea

In Korea, feral pigeons pose significant public health risks because they carry various zoonotic pathogens. Human population density is a significant factor in zoonotic disease events. Seoul is one of the largest cities by population density among developed countries and where most of the homeless population in Korea exists. We designed this study to compare the microbiota of pigeon feces by regional characteristics and the presence of homeless individuals. Therefore, this study used 16S rRNA amplicon sequencing to detect possible pathogenic microbes and assess the current risk of zoonosis in Seoul, South Korea. Pigeon fecal samples (n = 144) obtained from 19 public sites (86 and 58 fecal samples from regions in and outside Seoul, respectively) were examined. Potentially pathogenic bacteria were also detected in the fecal samples; Campylobacter spp. was found in 19 samples from 13 regions, Listeriaceae was found in seven samples, and Chlamydia spp. was found in three samples from two regions. Principal coordinates analysis and permutational multivariate analysis of variance revealed a significant difference in bacterial composition between the regions in Seoul (n = 86) and outside Seoul (n = 58) and between the regions with (n = 81) and without (n = 63) homeless individuals. Overall, this study identified various potentially pathogenic microorganisms in pigeon feces at public sites in South Korea. Moreover, this study demonstrates that the microbial composition was influenced by regional characteristics and homelessness. Taken together, this study provides important information for public health strategic planning and disease control.

The effects of antibiotics and illness on gut microbial composition in the fawn-footed mosaic-tailed rat (Melomys cervinipes)

The gut microbiota are critical for maintaining the health and physiological function of individuals. However, illness and treatment with antibiotics can disrupt bacterial community composition, the consequences of which are largely unknown in wild animals. In this study, we described and quantified the changes in bacterial community composition in response to illness and treatment with antibiotics in a native Australian rodent, the fawn-footed mosaic-tailed rat (Melomys cervinipes). We collected faecal samples during an undiagnosed illness outbreak in a captive colony of animals, and again at least one year later, and quantified the microbiome at each time point using 16s ribosomal rRNA gene sequencing. Gut bacterial composition was quantified at different taxonomic levels, up to family. Gut bacterial composition changed between time periods, indicating that illness, treatment with antibiotics, or a combination affects bacterial communities. While some bacterial groups increased in abundance, others decreased, suggesting differential effects and possible co-adapted and synergistic interactions. Our findings provide a greater understanding of the dynamic nature of the gut microbiome of a native Australian rodent species and provides insights into the management and ethical well-being of animals kept under captive conditions.

Flow-Based Fmoc-SPPS Preparation and SAR Study of Cathelicidin-PY Reveals Selective Antimicrobial Activity

Antimicrobial peptides (AMPs) hold promise as novel therapeutics in the fight against multi-drug-resistant pathogens. Cathelicidin-PY (NH₂-RKCNFLCKLKEKLRTVITSHIDKVLRPQG-COOH) is a 29-residue disulfide-cyclised antimicrobial peptide secreted as an innate host defence mechanism by the frog Paa yunnanensis (PY) and reported to possess broad-spectrum antibacterial and antifungal properties, exhibiting low cytotoxic and low hemolytic activity. Herein, we detail the total synthesis of cathelicidin-PY using an entirely on-resin synthesis, including assembly of the linear sequence by rapid flow Fmoc-SPPS and iodine-mediated disulfide bridge formation. By optimising a synthetic strategy to prepare cathelicidin-PY, this strategy was subsequently adapted to prepare a bicyclic head-to-tail cyclised derivative of cathelicidin-PY. The structure-activity relationship (SAR) of cathelicidin-PY with respect to the N-terminally positioned disulfide was further probed by preparing an alanine-substituted linear analogue and a series of lactam-bridged peptidomimetics implementing side chain to side chain cyclisation. The analogues were investigated for antimicrobial activity, secondary structure by circular dichroism (CD), and stability in human serum. Surprisingly, the disulfide bridge emerged as non-essential to antimicrobial activity and secondary structure but was amenable to synthetic modification. Furthermore, the synthetic AMP and multiple analogues demonstrated selective activity towards Gram-negative pathogen E. coli in physiologically relevant concentrations of divalent cations.

Red osier dogwood extract vs. trimethoprim-sulfadiazine (Part 2). Pharmacodynamic effects on ileal and cecal microbiota of broiler chickens challenged orally with Salmonella Enteritidis

With the subsisting restrictions on the use of antibiotics in poultry production, the use of plant extracts has shown some promising antimicrobial capacity similar to antibiotics; however, such capacity is largely dependent on their total polyphenol concentration and profile. Given the emerging antimicrobial potential of red osier dogwood (ROD) extract, the study aimed to investigate the pharmacodynamic effect of ROD extract on the ileal and cecal microbiota of broiler chickens challenged orally with Salmonella Enteritidis (SE). A 21 d 4 × 2 factorial experiment was conducted based on 2 main factors, including diets and SE challenge. A total of 384 one-day-old mixed-sex Cobb-500 broiler chicks were randomly allotted to 4 dietary treatments; Negative control (NC), NC + 0.075 mg trimethoprim-sulfadiazine (TMP/SDZ)/kg of diet, and NC containing either 0.3 or 0.5% ROD extract. On d 1, half of the birds were orally challenged with 0.5 mL of phosphate-buffered saline (Noninfected group) and the remaining half with 0.5 mL of 3.1 × 10⁵ CFU/mL SE (Infected group). Dietary treatments were randomly assigned to 8 replicate cages at 6 birds/cage. On d 21, 10 birds/treatment were euthanized and eviscerated to collect ileal and cecal digesta for gut microbiota analysis. The ileal and cecal microbiota was dominated by phyla Firmicutes, Proteobacteria, and Actinobacteriota. The SE infection decreased (P < 0.05) the relative abundance of Proteobacteria and Actinobacteriota in the ileum and ceca, respectively, however, it increased (P < 0.05) Proteobacteria in the ceca. Both 0.3 and 0.5% ROD extracts (P < 0.05) depressed the relative abundance of Actinobacteriota in the ileum but marginally improved (P < 0.05) it in the ceca compared to the TMP/SDZ treatment. Dietary TMP/SDZ increased (P < 0.05) genus Bifidobacterium at the ileal and cecal segments compared to other treatments. Dietary 0.3 and 0.5% marginally improved (P < 0.05) Bifidobacterium in the ceca and depressed (P < 0.05) Weissella and was comparably similar to TMP/SDZ in the ileum. Regardless of the dietary treatments and SE infection, alpha diversity differed (P < 0.05) between ileal and cecal microbiota. Beta diversity was distinct (P < 0.05) in both ileal and cecal digesta along the SE infection model. Conclusively, both ROD extract levels yielded a pharmacodynamic effect similar to antibiotics on ileal and cecal microbiota.

The gut microbiota in breast cancer development and treatment: The good, the bad, and the useful!

Regardless of the global progress in early diagnosis and novel therapeutic regimens, breast carcinoma poses a devastating threat, and the advances are somewhat marred by high mortality rates. Breast cancer risk prediction models based on the known risk factors are extremely useful, but a large number of breast cancers develop in women with no/low known risk. The gut microbiome exerts a profound impact on the host health and physiology and has emerged as a pivotal frontier in breast cancer pathogenesis. Progress in metagenomic analysis has enabled the identification of specific changes in the host microbial signature. In this review, we discuss the microbial and metabolomic changes associated with breast cancer initiation and metastatic progression. We summarize the bidirectional impact of various breast cancer-related therapies on gut microbiota and vice-versa. Finally, we discuss the strategies to modulate the gut microbiota toward a more favorable state that confers anticancer effects.

Microbiome–Gut Dissociation in the Neonate: Autism-Related Developmental Brain Disease and the Origin of the Placebo Effect

While the importance of the intestinal microbiome has been realised for a number of years, the significance of the phrase microbiota–gut–brain axis is only just beginning to be fully appreciated. Our recent work has focused on the microbiome as if it were a single entity, modifying the expression of the genetic inheritance of the individual by the generation of interkingdom signalling molecules, semiochemicals, such as dopamine. In our view, the purpose of the microbiome is to convey information about the microbial environment of the mother so as to calibrate the immune system of the new-born, giving it the ability to distinguish harmful pathogens from the harmless antigens of pollen, for example, or to help distinguish self from non-self. In turn, this requires the partition of nutrition between the adult and its microbiome to ensure that both entities remain viable until the process of reproduction. Accordingly, the failure of a degraded microbiome to interact with the developing gut of the neonate leads to failure of this partition in the adult: to low faecal energy excretion, excessive fat storage, and concomitant problems with the immune system. Similarly, a weakened gut–brain axis distorts interoceptive input to the brain, increasing the risk of psychiatric diseases such as autism. These effects account for David Barker’s 1990 suggestion of “the fetal and infant origins of adult disease”, including schizophrenia, and David Strachan’s 1989 observation of childhood immune system diseases, such as hay fever and asthma. The industrialisation of modern life is increasing the intensity and scale of these physical and psychiatric diseases and it seems likely that subclinical heavy metal poisoning of the microbiome contributes to these problems. Finally, the recent observation of Harald Brüssow, that reported intestinal bacterial composition does not adequately reflect the patterns of disease, would be accounted for if microbial eukaryotes were the key determinant of microbiome effectiveness. In this view, the relative success of “probiotic” bacteria is due to their temporary immune system activation of the gut–brain axis, in turn suggesting a potential mechanism for the placebo effect.

Prior antibiotics and risk of subsequent Herpes zoster: A population-based case control study

Background

The effect of antibiotics on the human microbiome is now well established, but their indirect effect on the related immune response is less clear. The possible association of Herpes zoster, which involves a reactivation of a previous varicella zoster virus infection, with prior antibiotic exposure might indicate a potential link with the immune response.

Methods

A case-control study was carried out using a clinical database, the UK’s Clinical Practice Research Datalink. A total of 163,754 patients with varicella zoster virus infection and 331,559 age/sex matched controls were identified and their antibiotic exposure over the previous 10 years, and longer when data permitted, was identified. Conditional logistic regression was used to identify the association between antibiotic exposure and subsequent infection in terms of volume and timing.

Results

The study found an association of antibiotic prescription and subsequent risk of varicella zoster virus infection (adjusted odds ratio of 1.50; 95%CIs: 1.42–1.58). The strongest association was with a first antibiotic over 10 years ago (aOR: 1.92; 95%CIs: 1.88–1.96) which was particularly pronounced in the younger age group of 18 to 50 (aOR 2.77; 95%CIs: 1.95–3.92).

Conclusions

By finding an association between prior antibiotics and Herpes zoster this study has shown that antibiotics may be involved in the reactivation of the varicella zoster virus. That effect, moreover, may be relatively long term. This indirect effect of antibiotics on viruses, possibly mediated through their effect on the microbiome and immune system, merits further study.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

Targeting the gut microbiome in the management of sepsis-associated encephalopathy

Brain injury resulting from sepsis, or sepsis-associated encephalopathy (SAE), occurs due to impaired end-organ perfusion, dysregulated inflammation affecting the central nervous system (CNS), blood-brain barrier (BBB) disruption, mitochondrial dysfunction, oxidative stress, accumulation of toxic neuropeptides and impaired toxin clearance secondary to sepsis-induced hepatic and renal dysfunction. The gut microbiome becomes pathologically altered in sepsis, which likely contributes to the pathogenesis of SAE. Herein, we review the literature detailing dysregulation of microbiota-gut-brain axis (MGBA) in SAE and highlight potential therapeutic strategies to modulate the gut microbiome to mitigate sepsis-induced brain injury.

Evaluation of genetic diversity of colistin-resistant Acinetobacter baumannii by BOX-PCR and ERIC-PCR: the first report

Aim: To control the spread of Acinetobacter baumannii in hospitals, it is necessary to identify the reservoir of organisms and the way they are transmitted. This study analyzed samples by BOX-PCR and enterobacterial repetitive intergenic consensus PCR techniques. Methods: Isolated strains were identified using the Microgen kit and blaOXA-51 gene. The genetic diversity of strains that were sensitive or resistant to colistin was evaluated by BOX-PCR and enterobacterial repetitive intergenic consensus PCR methods. Results: A total of 13% of the isolates were resistant to colistin, whereas 87% of the strains were sensitive to this medication. A. baumannii strains that were resistant or sensitive to colistin were divided into five groups using the BOX-PCR method and six groups using the enterobacterial repetitive intergenic consensus PCR method. Conclusion: Rapid identification and the use of appropriate tools to control colistin-resistant clones are essential to prevent the further spread of A. baumannii.

Microbiome–Gut Dissociation in the Neonate: Obesity and Coeliac Disease as Examples of Microbiome Function Deficiency Disorder

The purpose of this article is to provide a direction for translational research based on an analysis of the nature of complex, immune-related conditions such as obesity and coeliac disease. In essence, it seems that the prevalence of these non-communicable diseases is related to the degradation of the microbiome during the industrialisation of society, and that their nature can be used to infer the functions of the “pre-industrial” microbiome. Based on this analysis, the key point is the necessity for the fully functioning microbiome, acting alongside the parental genetic inheritance of the child, to be in place immediately after birth. In our view, this is achieved by the seemingly accidental process of maternal microbial inheritance during normal birth. Note, however, that this is not possible if the microbiome of the mother is itself degraded following previous problems. Under these conditions the health of a child may be affected from the moment of birth, although, with the exception of atopic diseases, such as eczema and food allergy, the consequences may not become apparent until late childhood or as an adult. In this way, this microbiome function deficiency hypothesis incorporates the epidemiological observations of David Strachan and David Barker in that their onset can be traced to early childhood. Coeliac disease has been chosen as an illustrative example of a multifactorial disorder due to the fact that, in addition to a series of immune system manifestations and a potential problem with food absorption, there is also a significant psychological component. Finally, it is worth noting that an ingestible sensor calibrated to the detection of interkingdom communication molecules (semiochemicals) within the intestine may offer a practical way of assessment and, perhaps, amelioration of at least some of the consequences of non-communicable disease.

1,4-Dihydropyridine as a Promising Scaffold for Novel Antimicrobials Against Helicobacter pylori

The increasing occurrence of multidrug-resistant strains of the gastric carcinogenic bacterium Helicobacter pylori threatens the efficacy of current eradication therapies. In a previous work, we found that several 1,4-dihydropyridine (DHP)-based antihypertensive drugs exhibited strong bactericidal activities against H. pylori by targeting the essential response regulator HsrA. To further evaluate the potential of 1,4-DHP as a scaffold for novel antimicrobials against H. pylori, we determined the antibacterial effects of 12 novel DHP derivatives that have previously failed to effectively block L- and T-type calcium channels. Six of these molecules exhibited potent antimicrobial activities (MIC ≤ 8 mg/L) against three different antibiotic-resistant strains of H. pylori, while at least one compound resulted as effective as metronidazole. Such antimicrobial actions appeared to be specific against Epsilonproteobacteria, since no deleterious effects were appreciated on Escherichia coli and Staphylococcus epidermidis. The new bactericidal DHP derivatives targeted the H. pylori regulator HsrA and inhibited its DNA binding activity according to both in vitro and in vivo analyses. Molecular docking predicted a potential druggable binding pocket in HsrA, which could open the door to structure-based design of novel anti-H. pylori drugs.

Impact of Therapeutics on Unified Immunity During Allergic Asthma and Respiratory Infections

Asthma is a common chronic respiratory disease that affects millions of people worldwide. Patients with allergic asthma, the most prevalent asthma endotype, are widely considered to possess a defective immune response against some respiratory infectious agents, including viruses, bacteria and fungi. Furthermore, respiratory pathogens are associated with asthma development and exacerbations. However, growing data suggest that the immune milieu in allergic asthma may be beneficial during certain respiratory infections. Immunomodulatory asthma treatments, although beneficial, should then be carefully prescribed to avoid misuse and overuse as they can also alter the host microbiome. In this review, we summarize and discuss recent evidence of the correlations between allergic asthma and the most significant respiratory infectious agents that have a role in asthma pathogenesis. We also discuss the implications of current asthma therapeutics beyond symptom prevention.

Cigarette Smoking and Human Gut Microbiota in Healthy Adults: A Systematic Review

The intestinal microbiota is a crucial regulator of human health and disease because of its interactions with the immune system. Tobacco smoke also influences the human ecosystem with implications for disease development. This systematic review aims to analyze the available evidence, until June 2021, on the relationship between traditional and/or electronic cigarette smoking and intestinal microbiota in healthy human adults. Of the 2645 articles published in PubMed, Scopus, and Web of Science, 13 were included in the review. Despite differences in design, quality, and participants’ characteristics, most of the studies reported a reduction in bacterial species diversity, and decreased variability indices in smokers’ fecal samples. At the phylum or genus level, the results are very mixed on bacterial abundance both in smokers and non-smokers with two exceptions. Prevotella spp. appears significantly increased in smokers and former smokers but not in electronic cigarette users, while Proteobacteria showed a progressive increase in Desulfovibrio with the number of pack-years of cigarette (p = 0.001) and an increase in Alphaproteobacteria (p = 0.04) in current versus never smokers. This attempt to systematically characterize the effects of tobacco smoking on the composition of gut microbiota gives new perspectives on future research in smoking cessation and on a new possible use of probiotics to contrast smoke-related dysbiosis.

Recent Advances in Understanding the Structure and Function of the Human Microbiome

Trillions of microbes live within our bodies in a deep symbiotic relationship. Microbial populations vary across body sites, driven by differences in the environment, immunological factors, and interactions between microbial species. Major advances in genome sequencing enable a better understanding of microbiome composition. However, most of the microbial taxa and species of the human microbiome are still unknown. Without revealing the identity of these microbes as a first step, we cannot appreciate their role in human health and diseases. A shift in the microbial balance, termed dysbiosis, is linked to a broad range of diseases from simple colitis and indigestion to cancer and dementia. The last decade has witnessed an explosion in microbiome research that led to a better understanding of the microbiome structure and function. This understanding leads to potential opportunities to develop next-generation microbiome-based drugs and diagnostic biomarkers. However, our understanding is limited given the highly personalized nature of the microbiome and its complex and multidirectional interactions with the host. In this review, we discuss: (1) our current knowledge of microbiome structure and factors that shape the microbial composition, (2) recent associations between microbiome dysbiosis and diseases, and (3) opportunities of new microbiome-based therapeutics. We analyze common themes, promises, gaps, and challenges of the microbiome research.

Effect of a synbiotic supplement as an antibiotic alternative on broiler skeletal, physiological, and oxidative parameters under heat stress

The aim of this study was to examine if synbiotics can function as alternatives to antibiotics in broiler production under heat stress (HS). Day-old broiler chicks (528 birds) were randomly placed in floor pens within 2 identical temperature-controlled rooms (11 birds/pen and 24 pens/room). The pens of each room were evenly divided among 3 treatments (n = 8): basal diet (CON), the basal diet mixed with 50 ppm of bacitracin methylene disalicylate (BMD) or a synbiotic (50 ppm of PoultryStar me^US, SYN). From d 15, room 2 was under thermoneutral (TN) conditions (TN-CON, TN-BMD, and TN-SYN), while HS was applied to room 1 at 32^oC for 9 hrs/d (0800 to 1700) (HS-CON, HS-BMD, and HS-SYN). Treatment effects on footpad dermatitis and gait score were measured on 5 birds/pen, and latency to lie (LTL) test was measured on 2 birds/pen at d 27 and d 41; and 1 broiler/pen was sampled on d 28 and d 42, respectively. Body, liver, and spleen weight were determined. Plasma levels of interleukins (IL), heat shock protein 70, immunoglobulin (Ig)Y, liver superoxide dismutase (SOD) and glutathione peroxidase (GPx) enzyme activities were examined. Heat stress suppressed BW and IgY concentrations on both d 28 and d 42, while suppressed plasma IL-6 concentrations, SOD activities, and LTL duration on d 28 only (P < 0.05). Among all treatments, SYN birds had the best foot and skeletal health scores on both d 27 and d 41 (P < 0.05). On d 42, SYN increased BW, and TN-SYN birds had higher relative spleen weight than both TN-BMD and TN-CON birds (P < 0.05). Antibiotic BMD increased BW (P < 0.05) but decreased SOD activities (P < 0.05) on d 42. These results indicate that the SYN supplementation decreases HS negative effect on broilers by improving BW, foot, and skeletal health, while BMD improves BW but also increases oxidative stress in broilers. The data suggest that synbiotic supplement may function as an alternative to antibiotics in broiler production during summer seasons, especially in the tropical and subtropical regions.

Europium Fluorescent Nanoparticles-Based Multiplex Lateral Flow Immunoassay for Simultaneous Detection of Three Antibiotic Families Residue

A fluorescent immunoassay based on europium nanoparticles (EuNPs-FIA) was developed for the simultaneous detection of antibiotic residues, solving the problems of single target detection and low sensitivity of traditional immunoassay methods. In the EuNPs-FIA, EuNPs were used as indictive probes by binding to anti-tetracyclines monoclonal antibodies (anti-TCs mAb), anti-sulphonamides monoclonal antibodies (anti-SAs mAb) and anti-fluoroquinolones monoclonal antibodies (anti-FQs mAb), respectively. Different artificial antigens were assigned to different regions of the nitrocellulose membrane as capture reagents. The EuNPs-FIA allowed for the simultaneous detection of three classes of antibiotics (tetracyclines, fluoroquinolones and sulphonamides) within 15 min. It enabled both the qualitative determination with the naked eye under UV light and the quantitative detection of target antibiotics by scanning the fluorescence intensity of the detection probes on the corresponding detection lines. For qualitative analysis, the cut-off values for tetracyclines (TCs), fluoroquinolones (FQs) and sulphonamides (SAs) were 3.2 ng/ml, 2.4 ng/ml and 4.0 ng/ml, respectively, which were much lower than the maximum residue limit in food. For quantitative analysis, these ranged from 0.06 to 6.85 ng/ml for TCs, 0.03–5.14 ng/ml for FQs, and 0.04–4.40 ng/ml for SAs. The linear correlation coefficients were higher than 0.97. The mean spiked recoveries ranged from 92.1 to 106.2% with relative standard deviations less than 8.75%. Among them, the three monoclonal antibodies could recognize four types of TCs, seven types of FQs and 13 types of SAs, respectively, and the detection range could cover 24 antibiotic residues with different structural formulations. The results of the detection of antibiotic residues in real samples using this method were highly correlated with those of high performance liquid chromatography (R² > 0.98). The accuracy and precision of the EuNPs-FIA also met the requirements for quantitative analysis. These results suggested that this multiplex immunoassay method was a promising method for rapid screening of three families of antibiotic residues.

The change of antibiotic susceptibility in febrile urinary tract infection in childhood and adolescence during the last decade

Purpose

The purpose of this study was to clarify the pattern of antibiotic resistance in pediatric urinary tract infections (UTIs).

Materials and Methods

We analyzed the data of entire urine culture tests and antibiotic susceptibility tests performed on hospitalized patients for febrile UTI at the Uijeongbu St. Mary’s Hospital during 2010–2020. A retrospective analysis was performed using medical records of urine culture results and antibiotic susceptibility results in patients with UTIs.

Results

We performed urine cultures from 2,491 patients, and identified bacterial types in 1,651 cases. We found that the resistance rates to ampicillin, ampicillin/sulbactam, cefazolin, gentamicin, piperacillin, tobramycin, and trimethoprim/sulfamethoxazole were already over 20% in 2010. The resistance rates to many other antibiotics also steadily increased over time. Among the antibiotics tested in 2020, only amikacin, cefoxitin, imipenem, piperacillin/tazobactam, and tigecycline showed the resistance rates below 20%. Noticeably, ciprofloxacin also showed an increase in the resistance rate from 7.3% in 2010 (S 139 vs. R 11) to 27.78% in 2019 (S 104 vs. R 40) and even over 30% (33.96%) in 2020 (S 35 vs. R 18).

Conclusions

Antibiotic resistance is a serious problem in pediatric UTIs. In the treatment of pediatric UTIs, more caution is needed in the use of antibiotics. It may be necessary to apply appropriate antibiotic management programs such as antibiotics steward program for pediatric patients. Failure of a proper response strategy coping with antibiotic resistance may accelerate the resistance crisis.

ANTIBIOTIC ASSOCIATIVE DISORDERS OF THE MICROBIOCENOSIS OF THE COLON IN INFANTS WITH ACUTE RESPIRATORY DISEASES

OBJECTIVE

The aim: Study the effect of antibiotics of different groups on the condition of the colon microflora in infants with acute respiratory pathology.

PATIENTS AND METHODS

Materials and methods: 140 infants with acute respiratory pathology were examined. Clinical, laboratory and instrumental examination, assessment of the functional state of all organs and systems, chest x ray, clinical signs of the colon microbiocenosis violation, analysis of bacteriological examination and immunological studies of local colon immunity (immunoglobulin concentration (sIgA, IgA, IgG, IgM) in coprofiltrates) were done.

RESULTS

Results: The negative effect of antibiotics of different pharmacological groups on the colon microflora state in infants with acute respiratory diseases has been established. The indigenous microflora of the colon is most inhibited by drugs from the group of 3rd generation cephalosporins, aminoglycosides and their combination. While cephalosporins 1-2nd generations, penicillins and macrolides to a lesser extent affect the state of the microbiocenosis of the colon. The use of two courses of antibacterial therapy to a greater extent disrupts the microbiocenosis of the colon in the examined children, compared with one course of therapy. In commune acquired pneumonia and acute complicated bronchiolitis in infants on the background of antibiotic therapy there is a probable decrease in secretory immunoglobulin in coprofiltrate (sIgA), compared with healthy children (p <0.05).

CONCLUSION

Conclusions: The analysis of the obtained results showed that antibiotic therapy negatively affects not only the condition of the colon microflora in the examined children, but also suppresses humoral factors of local immunity of the colonic mucosa. Key words: digestive tract microbiocenosis, antibiotic therapy, children.

Dietary grape pomace - effects on growth performance, intestinal health, blood parameters, and breast muscle myopathies of broiler chickens

The search for alternatives to antibiotics in poultry production is still on-going and has been directed towards investigation of the efficacy of different potential alternatives. However, it is important that the sought alternatives are cost-efficient and have no negative impact on meat quality, for ease of adoption and profit maximization. This study aimed at exploiting an agro-industrial waste, grape pomace (GP) as an alternative to in-feed antibiotics and assessing the effects on growth, intestinal morphology, ceca microbiota, ceca short-chain fatty acid (SCFA) concentration, blood biochemical parameters, and breast muscle myopathies of broiler chickens. A total of 576 one-day-old Cobb-500 broiler chicks were randomly allotted to 3 dietary treatments - Negative control (NC, a corn-wheat soybean-based diet), NC + 0.05% bacitracin methylene disalicylate (BMD), and NC + 2.5% GP. Each treatment was assigned to 8 replicate pens with 25 birds per pen. Body weight (BW), feed intake (FI), and feed conversion ratio (FCR) were determined weekly. On d 36, 2 chickens/pen were euthanized for measuring blood biochemical parameters, ceca SCFA, and ceca microbiota. White striping (WS) and wooden breast (WB) incidence were assessed in 4 chickens/pen on d 42. The GP diet increased (P < 0.05) average FI throughout the feeding phases compared to the other treatments, but overall FCR was similar. Birds in the GP treatment had higher (P < 0.05) villus height (VH) and increased VH:crypt depth ratio in the duodenum and jejunum compared to other treatments. The level of ceca SCFA and the incidence of WS and WB was the same for all treatments. Plasma Ca and P were significantly higher (P < 0.05) in birds fed GP and BMD, compared to the NC. Birds in the GP treatment had significantly reduced (P < 0.05) plasma aspartate transaminase than other treatments. Birds receiving GP had a higher (P < 0.05) relative abundance of the phylum Bacteroidetes and reduced (P < 0.05) Firmicutes compared to other treatments. The relative abundance of Bacteroides and Lactobacillus genera were higher (P < 0.05) among birds fed GP compared to other treatments. Inclusion of 2.5% GP in broiler chicken diets improved gut morphology and modified the cecal bacterial community and blood biochemical profiles with no adverse effect on growth performance and meat quality.

Cross-Sectional Analysis of the Microbiota of Human Gut and Its Direct Environment in a Household Cohort with High Background of Antibiotic Use

Comprehensive insight into the microbiota of the gut of humans and animals, as well as their living environment, in communities with a high background of antibiotic use and antibiotic resistance genes is scarce. Here, we used 16S rRNA gene sequencing to describe the (dis)similarities in the microbiota of feces from humans (n = 107), domestic animals (n = 36), water (n = 89), and processed food (n = 74) in a cohort with individual history of antibiotic use in northern Vietnam. A significantly lower microbial diversity was observed among individuals who used antibiotics in the past 4 months (n = 44) compared to those who did not (n = 63). Fecal microbiota of humans was more diverse than nonhuman samples and shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4% (3.2–9.9)), water (2.2% (1.2–2.8)), and food (3.1% (1.5–3.1)). Sharing of ASVs between humans and companion animals was not associated with the household. However, we did observe a correlation between an Enterobacteriaceae ASV and the presence of extended-spectrum beta-lactamase CTX-M-group-2 encoding genes in feces from humans and animals (p = 1.6 × 10⁻³ and p = 2.6 × 10⁻², respectively), hinting toward an exchange of antimicrobial-resistant strains between reservoirs.

Oral iron supplementation after antibiotic exposure induces a deleterious recovery of the gut microbiota

Background

Oral iron supplementation is commonly prescribed for anemia and may play an important role in the gut microbiota recovery of anemic individuals who received antibiotic treatment. This study aims to investigate the effects of iron supplementation on gut microbiota recovery after antibiotics exposure.

Results

Mice were subjected to oral antibiotic treatment with neomycin and metronidazole and were fed diets with different concentrations of iron. The composition of the gut microbiota was followed throughout treatment by 16S rRNA sequencing of DNA extracted from fecal samples. Gut microbiota functions were inferred using PICRUSt2, and short-chain fatty acid concentration in fecal samples was assessed by liquid-chromatography mass spectrometry. Iron supplementation after antibiotic exposure shifted the gut microbiota composition towards a Bacteroidetes phylum-dominant composition. At the genus level, the iron-supplemented diet induced an increase in the abundance of Parasutterella and Bacteroides, and a decrease of Bilophila and Akkermansia. Parasutterella excrementihominis, Bacteroides vulgatus, and Alistipes finegoldii, were more abundant with the iron excess diet. Iron-induced shifts in microbiota composition were accompanied by functional modifications, including an enhancement of the biosynthesis of primary bile acids, nitrogen metabolism, cyanoamino acid metabolism and pentose phosphate pathways. Recovery after antibiotic treatment increased propionate levels independent of luminal iron levels, whereas butyrate levels were diminished by excess iron.

Conclusions

Oral iron supplementation after antibiotic therapy in mice may lead to deleterious changes in the recovery of the gut microbiota. Our results have implications on the use of oral iron supplementation after antibiotic exposure and justify further studies on alternative treatments for anemia in these settings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02320-0.