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

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.

Effect of Intrapartum Antibiotics Prophylaxis on the Bifidobacterial Establishment within the Neonatal Gut

Antibiotics are important disruptors of the intestinal microbiota establishment, linked to immune and metabolic alterations. The intrapartum antibiotics prophylaxis (IAP) is a common clinical practice that is present in more than 30% of labours, and is known to negatively affect the gut microbiota composition. However, little is known about how it affects to Bifidobacterium (sub)species level, which is one of the most important intestinal microbial genera early in life. This study presents qualitative and quantitative analyses of the bifidobacterial (sub)species populations in faecal samples, collected at 2, 10, 30 and 90 days of life, from 43 healthy full-term babies, sixteen of them delivered after IAP use. This study uses both 16S rRNA–23S rRNA internal transcribed spacer (ITS) region sequencing and q-PCR techniques for the analyses of the relative proportions and absolute levels, respectively, of the bifidobacterial populations. Our results show that the bifidobacterial populations establishment is affected by the IAP at both quantitative and qualitative levels. This practice can promote higher bifidobacterial diversity and several changes at a compositional level. This study underlines specific targets for developing gut microbiota-based products for favouring a proper bifidobacterial microbiota development when IAP is required.

Do Antibiotics Cause Obesity Through Long-term Alterations in the Gut Microbiome? A Review of Current Evidence

PURPOSE OF REVIEW

In this review, we summarize current evidence on the association between antibiotics and the subsequent development of obesity through modulation of the gut microbiome. Particular emphasis is given on (i) animal and human studies and their limitations; (ii) the reservoir of antibiotics in animal feed, emerging antibiotic resistance, gut dysbiosis, and obesity; (iii) the role of infections, specifically viral infections, as a cause of obesity; and (iv) the potential therapeutic approaches other than antibiotics to modulate gut microbiome.

RECENT FINDINGS

Overall, the majority of animal studies and meta-analyses of human studies on the association between antibiotics and subsequent development of obesity are suggestive of a link between exposure to antibiotics, particularly early exposure in life, and the development of subsequent obesity as a result of alterations in the diversity of gut microbiota. The evidence is strong in animal models whereas evidence in humans is inconclusive requiring well-designed, long-term longitudinal studies to examine this association. Based on recent meta-analyses and epidemiologic studies in healthy children, factors, such as the administration of antibiotics during the first 6 months of life, repeated exposure to antibiotics for ≥ 3 courses, treatment with broad-spectrum antibiotics, and male gender have been associated with increased odds of overweight/obesity. Early antibiotic exposure in animal models has shown that reductions in the population size of specific microbiota, such as Lactobacillus, Allobaculum, Rikenellaceae, and Candidatus Arthromitus, are related to subsequent adiposity. These data suggest that the loss of diversity of the gut microbiome, especially early in life, may have potential long-term detrimental effects on the adult host gut microbiome and metabolic health. Genetic, environmental, and age-related factors influence the gut microbiome throughout the lifetime. More large-scale, longer-term, longitudinal studies are needed to determine whether changes that occur in the microbiome after exposure to antibiotics, particularly early exposure, are causal of subsequent weight gain or consequent of weight gain in humans. Further well-designed, large-scale RCTs in humans are required to evaluate the effects of administration of antibiotics, particularly early administration, and the subsequent development of overweight/obesity. Therapeutic interventions, such as bacteriophage treatment or the use of probiotics, especially genetically engineered ones, need to be evaluated in terms of prevention and management of obesity.

Contribution of the Commensal Microflora to the Immunological Homeostasis and the Importance of Immune-Related Drug Development for Clinical Applications

Not long ago, self-reactive immune activity was considered as pathological trait. A paradigm shift has now led to the recognition of autoimmune processes as part of natural maintenance of molecular homeostasis. The immune system is assigned further roles beneath the defense against pathogenic organisms. Regarding the humoral immune system, the investigation of natural autoantibodies that are frequently found in healthy individuals has led to further hypotheses involving natural autoimmunity in other processes as the clearing of cellular debris or decrease in inflammatory processes. However, their role and origin have not been entirely clarified, but accumulating evidence links their formation to immune reactions against the gut microbiome. Antibodies targeting highly conserved proteins of the commensal microflora are suggested to show self-reactive properties, following the paradigm of the molecular mimicry. Here, we discuss recent findings, which demonstrate potential links of the commensal microflora to the immunological homeostasis and highlight the possible implications for various diseases. Furthermore, specific components of the immune system, especially antibodies, have become a focus of attention for the medical management of various diseases and provide attractive treatment options in the future. Nevertheless, the development and optimization of such macromolecules still represents a very time-consuming task, shifting the need to more medical agents with simple structural properties and low manufacturing costs. Synthesizing only the biologically active sites of antibodies has become of great interest for the pharmaceutical industry and offers a wide range of therapeutic application areas as it will be discussed in the present review article.

Subinhibitory concentrations of nalidixic acid alter bacterial physiology and induce anthropogenic resistance in a commensal strain of Escherichia coli in vitro

The human gut houses a complex group of bacterial genera, including both opportunistic pathogens and commensal micro-organisms. These are regularly exposed to antibiotics, and their subinhibitory concentrations play a pivotal role in shaping the microbial responses. This study was aimed to investigate the effects exerted by sub-MICs of nalidixic acid (NA) on the growth rate, bacterial motility, biofilm formation and expression of outer membrane proteins (OMPs) in a commensal strain of E. coli. The NA-sensitive strain was sequentially passaged under sub-MICs of NA. E-test was used to determine the MIC values of NA. Results indicated significant changes in the growth profile of commensal E. coli upon exposure to NA at sub-MICs. Differential expression of OMPs was observed in cells treated with sub-MICs of NA. Bacterial motility was reduced under 1/2 MIC of NA. Interestingly, successive passaging under 1/2 MIC of NA led to the emergence of resistant E. coli with an increased MIC value of 64 µg ml^-1 in just 24 days. The NA-resistant variant was confirmed by comparing its 16S rRNA sequence to that of the sensitive commensal strain. Mutations in the Quinolone Resistance-Determining Regions (QRDRs) of chromosomal gyrA, and Topoisomerase IV-encoding parC genes were detected in NA-resistant E. coli. Our results demonstrate how antibiotics play an important role as signalling molecules or elicitors in driving the pathogenicity of commensal bacteria in vitro.

Effects of Erythromycin on Osteoclasts and Bone Resorption via DEL-1 Induction in Mice

Macrolides are used to treat various infectious diseases, including periodontitis. Furthermore, macrolides are known to have immunomodulatory effects; however, the underlying mechanism of their action remains unclear. DEL-1 has emerged as an important factor in homeostatic immunity and osteoclastogenesis. Specifically, DEL-1 is downregulated in periodontitis tissues. Therefore, in the present study, we investigated whether the osteoclastogenesis inhibitory effects of erythromycin (ERM) are mediated through upregulation of DEL-1 expression. We used a ligature-induced periodontitis model in C57BL/6Ncrl wild-type or DEL-1-deficient mice and in vitro cell-based mechanistic studies to investigate how ERM inhibits alveolar bone resorption. As a result of measuring alveolar bone resorption and gene expression in the tooth ligation model, ERM treatment reduced bone loss by increasing DEL-1 expression and decreasing the expression of osteoclast-related factors in wild-type mice. In DEL-1-deficient mice, ERM failed to suppress bone loss and gene expression of osteoclast-related factors. In addition, ERM treatment downregulated osteoclast differentiation and calcium resorption in in vitro experiments with mouse bone marrow-derived macrophages. In conclusion, ERM promotes the induction of DEL-1 in periodontal tissue, which may regulate osteoclastogenesis and decrease inflammatory bone resorption. These findings suggest that ERM may exert immunomodulatory effects in a DEL-1-dependent manner.