The impact of the gut microbiota on drug metabolism and clinical outcome

The significance of the gut microbiota as a determinant of drug pharmacokinetics and accordingly therapeutic response is of increasing importance with the advent of modern medicines characterised by low solubility and/or permeability, or modified-release. These physicochemical properties and release kinetics prolong drug residence times within the gastrointestinal tract, wherein biotransformation by commensal microbes can occur. As the evidence base in support of this supplementary metabolic “organ” expands, novel opportunities to engineer the microbiota for clinical benefit have emerged. This review provides an overview of microbe-mediated alteration of drug pharmacokinetics, with particular emphasis on studies demonstrating proof of concept in vivo. Additionally, recent advances in modulating the microbiota to improve clinical response to therapeutics are explored.

Growing up in a bubble: using germ-free animals to assess the influence of the gut microbiota on brain and behavior

There is a growing recognition of the importance of the commensal intestinal microbiota in the development and later function of the central nervous system. Research using germ-free mice (mice raised without any exposure to microorganisms) has provided some of the most persuasive evidence for a role of these bacteria in gut-brain signalling. Key findings show that the microbiota is necessary for normal stress responsivity, anxiety-like behaviors, sociability, and cognition. Furthermore, the microbiota maintains central nervous system homeostasis by regulating immune function and blood brain barrier integrity. Studies have also found that the gut microbiota influences neurotransmitter, synaptic, and neurotrophic signalling systems and neurogenesis. The principle advantage of the germ-free mouse model is in proof-of-principle studies and that a complete microbiota or defined consortiums of bacteria can be introduced at various developmental time points. However, a germ-free upbringing can induce permanent neurodevelopmental deficits that may deem the model unsuitable for specific scientific queries that do not involve early-life microbial deficiency. As such, alternatives and complementary strategies to the germ-free model are warranted and include antibiotic treatment to create microbiota-deficient animals at distinct time points across the lifespan. Increasing our understanding of the impact of the gut microbiota on brain and behavior has the potential to inform novel management strategies for stress-related gastrointestinal and neuropsychiatric disorders.

Behavioural and neurochemical consequences of chronic gut microbiota depletion during adulthood in the rat

Gut microbiota colonization is a key event for host physiology that occurs early in life. Disruption of this process leads to altered brain development which ultimately manifests as changes in brain function and behaviour in adulthood. Studies using germ-free mice highlight the extreme impact on brain health that results from life without commensal microbes, however the impact of microbiota disturbances occurring in adulthood is less studied. To this end, we depleted the gut microbiota of 10-week-old male Sprague Dawley rats via chronic antibiotic treatment. Following this marked, sustained depletion of the gut bacteria, we investigated behavioural and molecular hallmarks of gut-brain communication. Our results reveal that depletion of the gut microbiota during adulthood results in deficits in spatial memory as tested by Morris water maze, increased visceral sensitivity and a greater display of depressive-like behaviours in the forced swim test. In tandem with these clear behavioural alterations we found change in altered CNS serotonin concentration along with changes in the mRNA levels of corticotrophin releasing hormone receptor 1 and glucocorticoid receptor. Additionally, we found changes in the expression of BDNF, a hallmark of altered microbiota-gut-brain axis signaling. In summary, this model of antibiotic-induced depletion of the gut microbiota can be used for future studies interested in the impact of the gut microbiota on host health without the confounding developmental influence of early-life microbial alterations.

Establishment and development of infant gut microbiota

The nascent gut microbiota at birth is established in concert with numerous developmental parameters. Here, in the INFAMTET study, we chronicled the impact of some factors which are key determinants of the infant gut microbiota, namely; mode of birth, gestational age, and type of feeding. We determined that the aggregated microbiota profile of naturally delivered, initially breastfed infants are relatively stable from one week to six months of age and are not significantly altered by increased duration of breastfeeding. Contrastingly, there is significant development of the microbiota profile of C-section delivered infants, and this development is significantly influenced by breastfeeding duration. Preterm infants, born by either mode of birth, initially have a high proportion of Proteobacteria, and demonstrate significant development of the gut microbiota from week 1 to later time-points. The microbiota is still slightly, but significantly, affected by birth mode at one year of age although no specific genera were found to be significantly altered in relative abundance. By two years of age, there is no effect of either birth mode or gestational age. However this does not preclude the possibility that symptoms developed later in life, which are associated with preterm or C-section birth, are as a result of the early perturbation of the neonatal gut microbiota. It is likely that the combination of relatively low exposure (breast fed), high exposure (formula fed) or delayed exposure (C-section and preterm) to specific antigens and the resulting inflammatory responses, in this crucial window of host-microbiota interaction, influence systemic health of the individual throughout life.

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

Background: Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults. Results: Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week's storage compared to immediately extracted samples. After 2 weeks' storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (p

Impact of salt reduction on biogenic amines, fatty acids, microbiota, texture and sensory profile in traditional blood dry-cured sausages

Meat industry needs to reduce salt in their products due to health issues. The present study evaluated the effect of salt reduction from 6% to 3% in two Portuguese traditional blood dry-cured sausages. Physicochemical and microbiological parameters, biogenic amines, fatty acids and texture profiles and sensory panel evaluations were considered. Differences due to salt reduction were perceptible in a faint decline of water activity, which slightly favoured microbial growth. Total biogenic amines content ranged from 88.86 to 796.68 mg kg 1 fresh matter, with higher amounts, particularly of cadaverine, histamine and tyramine, in low-salt products. Still, histamine and other vasoactive amines remained at low levels, thus not affecting consumers’ health. Regarding fatty acids, no significant differences were observed due to salt. However, texture profile analysis revealed lower resilience and cohesiveness in low-salt products, although no textural changes were observed by the sensory panel. Nevertheless, low-salt sausages were clearly preferred by panellists.

Avaliação do impacto de eventos comerciais de milho Bt sobre a microbiota do solo.

2016

Impacto do manejo agrícola sobre a microbiota do solo.

Para avaliar o efeito do manejo agrícola de solo sobre os parâmetros biológico, bioquímico e químico, três propriedades agrícolas de Suzano/SP foram selecionadas contendo os seguintes tratamentos: áreas de manejo biodinâmico com o cultivo de hortaliças, áreas de manejo convencional com o cultivo de milho, área de pastagem (8 anos) e área de mata nativa. Amostras de solo foram submetidas as analises química, bioquímica e biológica. Os resultados mostraram que alguns parâmetros biológicos (bactérias esporulantes, actinomicetos, microrganismos celulolíticos), químico (pH, CTC, MO) e bioquímico (desidrogenase, polissacarídeos) foram superiores nas áreas de manejo biodinâmico em relação ao manejo convencional.

Microbiologia ambiental.

Impacto de mudanças climáticas globais sobre a microbiota terrestre - Raquel Ghini. Impacto de xenobióticos e metais pesados na microbiota do solo - Célia Maria Maganhotto de Souza Silva e Rosana Faria Vieira. Microrganismos, minerais e metais - Oswaldo Garcia Jr. e Denise Bevilaqua. Bioprospecção da diversidade microbiana cultivável e não cultivável - Raquel Silva Peixoto, Alexandre Soares Rosado e Rodrigo Gouvêa Taketani. Técnicas moleculares aplicadas aos estudos de ecologia microbiana: A PCR em tempo real - Paulo Teixeira Lacava e João Lúcio de Azevedo. Biofilmes microbianos - René P Schneider. Biossurfactantes - Fátima Menezes Bento, Flavio A. de Oliveira Camargo e Christine Claire Gaylarde. Importância ambiental da biocatálise - Viridiana Santana Ferreira-Leitão, Maria Antonieta Ferrara e Elba P S. Bom. Estratégias de isolamento de microrganismos envolvidos na degradação de xenobióticos - Itamar Soares de Melo e João Lúcio de Azevedo. Biodegradação anaeróbia - Rosana Filomena Vazoller, Márcia Helena Rissato Zamariolli Damianovic e Juliana Calábria Araújo. Biodegradação de compostos aromáticos - Aneli de Melo Barbosa, Ellen Cristine Giese e Luiz Gustavo Covizzi. Biodegradação de organoclorados no solo por basidiomicetos lignovelulolíticos - Vera Lúcia Ramos Bonomi, Kátia Maria Gomes Machado, Dácio Roberto Mateus e Vera Maria Vitali. Biodegradação de lignina e tratamento de efluentes por fungos ligninolíticos: atualização - Nelson Durán e Elisa Esposito. Biodegradação de corantes têxteis - Priscila Maria Dellamatrice, Regina Teresa Rosim Monteiro e Doralice de Souza Luro Balan. Biodegradação de superfícies pintadas - Denise de Souza Saad. Biodegradação de polímeros sintéticos - Sandra Mara Martins Franchetti, José Carlos Marconato e Adriana de Campos. Biodegradação de fungicidas - Célia Maria Maganhotto de Souza Silva, Elisabeth Francisconi Fay e Rosângela Blotta Abakerli. Biodegradação de monoterpenos - Lucia Regina Durrant. Degradação de cafeína por bactérias - Paulo Mazzafera e Dirce Mithico Yamaoka-Yano. Degradação abiótica de xenobióticos - Elisabeth Francisconi Fay, Célia Maria Maganhotto de Souza Silva e Itamar Soares de Melo. Biodeterioração no ambiente construído - Márcia A. Shirakawa, Vanderley M. John e Maria Alba Cincotto. Biodeterioração de monumentos históricos - Maria Aparecida de Resende. Biodeterioração de monumentos históricos - Maria Aparecida de Resende. Biorremediação de solos contaminados por petróleo e derivados - Paulo Negrais Seabra. Fitorremediação de metais - Marcia Pletsch, Á ndrea C. A. Barros e Brancilene S. de Araujo. Importância da rizosfera na biodegradação de xenobióticos - Itamar Soares de Melo. Microbiologia aquática marinha - Irnia Nelly G. Rivera, Claudete Rodrigues Paula e Claudiana Paula de Souza. Transferência horizontal de genes de plantas geneticamente modificadas: avaliação dos riscos para as comunidades microbianas - Welington Luiz Araújo, Priscilla de Barros Rossetto e Júlia Ifuklinsky-Sobral.

Impacto de mudanças climáticas globais sobre a microbiota terrestre.

2008

Impacto de xenobióticos e metais pesados na microbiota do solo.

2008

A review of the pharmacobiotic regulation of gastrointestinal inflammation by probiotics, commensal bacteria and prebiotics.

The idea that microbes induce disease has steered medical research toward the discovery of antibacterial products for the prevention and treatment of microbial infections. The twentieth century saw increasing dependency on antimicrobials as mainline therapy accentuating the notion that bacterial interactions with humans were to be avoided or desirably controlled. The last two decades, though, have seen a refocusing of thinking and research effort directed towards elucidating the critical inter-relationships between the gut microbiome and its host that control health/wellness or disease. This research has redefined the interactions between gut microbes and vertebrates, now recognizing that the microbial active cohort and its mammalian host have shared co-evolutionary metabolic interactions that span millennia. Microbial interactions in the gastrointestinal tract provide the necessary cues for the development of regulated pro- and anti-inflammatory signals that promotes immunological tolerance, metabolic regulation and other factors which may then control local and extra-intestinal inflammation. Pharmacobiotics, using nutritional and functional food additives to regulate the gut microbiome, will be an exciting growth area of therapeutics, developing alongside an increased scientific understanding of gut-microbiome symbiosis in health and disease.

Development and validation of a ultra performance LC-ESI/MS method for analysis of metabolic phenotypes of healthy men in day and night urine samples

Ultra-performance LC coupled to quadrupole TOF/MS (UPLC-QTOF/MS) in positive and negative ESI was developed and validated to analyze metabolite profiles for urine from healthy men during the day and at night. Data analysis using principal components analysis (PCA) revealed differences between metabolic phenotypes of urine in healthy men during the day and at night. Positive ions with mass-to-charge ratio (m/z) 310.24 (5.35 min), 286.24 (4.74 min) and 310.24 (5.63 min) were elevated in the urine from healthy men at night compared to that during the day. Negative ions elevated in day urine samples of healthy men included m/z 167.02 (0.66 min), 263.12 (2.55 min) and 191.03 (0.73 min), whilst ions m/z 212.01 (4.77 min) were at a lower concentration in urine of healthy men during the day compared to that at night. The ions m/z 212.01 (4.77 min), 191.03 (0.73 min) and 310.24 (5.35 min) preliminarily correspond to indoxyl sulfate, citric acid and N-acetylneuraminic acid, providing further support for an involvement of phenotypic difference in urine of healthy men in day and night samples, which may be associated with notably different activities of gut microbiota, velocity of tricarboxylic acid cycle and activity of sialic acid biosynthesis in healthy men as regulated by circadian rhythm of the mammalian bioclock.

Promiscuity, pheromones and pathogenicity : why all Enterococci are not created equal

Enterococcus faecalis is a Gram-positive, coccus shaped, lactic acid bacterium, with demonstrated ubiquity across multiple anatomical sites. Enterococcus faecalis isolates have been isolated from clinical samples as the etiological agent in patients with overt infections, and from body sites previously thought to be sterile but absent of signs and symptoms of infection. E. faecalis is implicated in both human health and disease, recognized as a commensal, a probiotic and an opportunistic multiply resistant pathogen. E. faecalis has emerged as a key pathogen in nosocomial infections. E. faecalis is well equipped to avert recognition by host cell immune mediators. Antigenic cell wall components including lipotechoic acids are concealed from immune detection by capsular polysaccharides produced by some strains. Thereby preventing complement activation, the pro-inflammatory response, opsonisation and phagocytosis. E. faecalis also produces a suite of enzymes including gelatinase and cytolysin, which aid in both virulence and host immune evasion. The ability of enterococci to form biofilms in vivo further increases virulence, whilst simultaneously preventing detection by host cells. E. faecalis exhibits high levels of both intrinsic and acquired antimicrobial resistance. The mobility of the E. faecalis genome is a significant contributor to antimicrobial resistance, with this species also transferring resistance to other Gram-positive bacteria. Whilst E. faecalis is of increasing concern in nosocomial infections, its role as a member of the endogenous microbiota cannot be underestimated. As a commensal and probiotic, E. faecalis plays an integral role in modulating the immune response, and in providing endogenous antimicrobial activity to enhance exclusion or inhibition of opportunistic pathogens in certain anatomical niches. In this chapter we will review possible mediators of enterococcal transition from commensal microbe to opportunistic pathogen, considering isolates obtained from patients diagnosed with pathogenic infections and those obtained from asymptomatic patients.

Prevalence of methicillin resistance and virulence determinants of Staphylococcus aureus in diabetic foot ulcers

Background Diabetic foot ulceration (DFU) is a multifactorial process and is responsible for considerable morbidity and contributes to the increasing cost of health care worldwide. The diagnosis and identification of these ulcers remains a complex problem. Bacterial infection is promoted in the diabetic foot wound by decreased vascular supply and impaired host immune response. As conventional clinical microbiological methods are time-consuming and only identifies about 1% of the wound microbiota, detection of bacteria present in DFUs using molecular methods is highly advantageous and efficient. The aim of this study was to assess the virulence and methicillin resistance profiles of Staphylococcus aureus detected in DFUs using DNA-based methods. Methods A total of 223 swab samples were collected from 30 patients from March to October 2012. Bacterial DNA was extracted from the swab samples using standard procedures and was used to perform polymerase chain reaction (PCR) using specific oligonucleotide primers. The products were visualized using agarose gel electrophoresis. Results S. aureus was detected in 44.8% of samples. 25% of the S. aureus was methicillin-resistant S. aureus harboring the mecA gene. The alpha-toxin gene was present in 85% of the S. aureus positive samples. 61% of the S. aureus present in DFU samples harbored the exfoliatin factor A gene. Both the fibronectin factor A and fibronectin factor B gene were detected in 71% and 74% of the S. aureus positive samples. Conclusions DNA-based detection and characterization of bacteria in DFUs are rapid and efficient and can assist in accurate, targeted antibiotic therapy of DFU infections. The majority of S. aureus detected in this study were highly virulent and also resistant to methicillin. Further studies are required to understand the role of S. aureus in DFU trajectory.