Special issue : The Human Intestinal Microbiota

Peer reviewed

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment

IA, JNP, and MP were partly supported by the NIH, grants R01-AI-100947 to MP, and R21-GM-107683 to Matthias Chung, subcontract to MP. JNP was partly supported by an NSF graduate fellowship number DGE750616. IA, JNP, BRL, OCS and MP were supported in part by the Bill and Melinda Gates Foundation, award number 42917 to OCS. JP and AWW received core funding support from The Wellcome Trust (grant number 098051). AWW, and the Rowett Institute of Nutrition and Health, University of Aberdeen, receive core funding support from the Scottish Government Rural and Environmental Science and Analysis Service (RESAS).

Análise da microbiota intestinal em adultos com hábitos alimentares distintos e de associações com a inflamação e resistência à insulina

Introdução: A microbiota intestinal possui grande diversidade de bactérias, predominantemente dos filos Bacteroidetes e Firmicutes, com múltiplas funções. A alimentação pode alterar sua composição e função. Alto teor de gordura saturada altera a permeabilidade intestinal, eleva os lipopolissacarídeos e predispõe à inflamação subclínica crônica. Dieta rica em fibras, como a vegetariana, induz elevação de ácidos graxos de cadeia curta e benefícios metabólicos. Objetivos: Para analisar a composição da microbiota intestinal de adventistas com diferentes hábitos alimentares e associá-los à inflamação subclínica e resistência à insulina, esta tese incluiu: 1) revisão dos mecanismos que associam a alimentação à microbiota intestinal e ao risco cardiometabólico; 2) verificação da composição da microbiota intestinal segundo diferentes hábitos alimentares e de associações com biomarcadores de doenças cardiometabólicas; 3) avaliação da associação entre a abundância de Akkermansia muciniphila e o metabolismo da glicose; 4) análise da presença de enterótipos e de associações com características clínicas. Métodos: Este estudo transversal incluiu 295 adventistas estratificados segundo hábitos alimentares (vegetariano estrito, ovo-lacto-vegetariano e onívoro). Foram avaliadas associações com dados clínicos, bioquímicos e inflamatórios. O perfil da microbiota foi obtido por sequenciamento do gene 16S rRNA (Illumina® Miseq). Resultados: 1) Há evidências de que as relações entre dieta, inflamação, resistência à insulina e risco cardiometabólico são em parte mediadas pela composição da microbiota intestinal. 2) Vegetarianos apresentaram melhor perfil clínico quando comparados aos onívoros. Confirmou-se maior abundância de Firmicutes e Bacteroidetes, que não diferiram segundo a adiposidade corporal. Entretanto, vegetarianos estritos apresentaram mais Bacteroidetes, menos Firmicutes e maior abundância do gênero Prevotella quando comparados aos outros dois grupos de hábitos alimentares. Entre os ovo-lactovegetarianos verificou-se maior proporção de Firmicutes especialmente do gênero Faecalibacterium. Nos onívoros, houve super-representação do filo Proteobacteria (Succinivibrio e Halomonas) comparados aos vegetarianos. 3) Indivíduos normoglicêmicos apresentaram maior abundância de Akkermansia muciniphila que aqueles com glicemia alterada. A abundância desta bactéria correlacionou-se inversamente à glicemia e hemoglobina glicosilada. 4) Foram identificados três enterótipos (Bacteroides, Prevotella e Ruminococcaceae), similares àqueles previamente descritos. As concentrações de LDL-C foram menores no enterótipo 2, no qual houve maior frequência de vegetarianos estritos. Discussão: 1) Conhecimentos sobre participação da microbiota na fisiopatologia de doenças poderão reverter em estratégias para manipulá-la para promover saúde. 2) Apoia-se a hipótese de que hábitos alimentares se associam favorável ou desfavoravelmente a características metabólicas e inflamatórias do hospedeiro via alterações na composição da microbiota intestinal. Sugerimos que a exposição a alimentos de origem animal possa impactar negativamente nas proporções de comunidades bacterianas. 3) Sugerimos que a abundância da Akkermansia muciniphila possa participar do metabolismo da glicose. 4) Reforçamos que a existência de três enterótipos não deva ser específica de certas populações/continentes. Apesar de desconhecido o significado biológico destes agrupamentos, as correlações com o perfil lipídico podem sugerir sua utilidade na avaliação do risco cardiometabólico. Conclusões: Nossos achados fortalecem a ideia de que a composição da microbiota intestinal se altera mediante diferentes hábitos alimentares, que, por sua vez, estão associados a alterações nos perfis metabólicos e inflamatórios. Estudos prospectivos deverão investigar o potencial da dieta na prevenção de distúrbios cardiometabólicos mediados pela microbiota.

Interactions of maize bushy stunt phytoplasma with the leafhopper vector, Dalbulus maidis (Delong and Wolcott) (Hemiptera: Cicadellidae) and associated microbiota

Phytoplasmas are bacteria with a persistent propagative transmission by insect vectors that generates direct and indirect interactions among them. In order to understand these interactions for maize bushy stunt phytoplasma (MBSP) and the leafhopper vector Dalbulus maidis (Hemiptera: Cicadellidae), two research lines were addressed. The first one aimed to determine the indirect effects of maize infection by MBSP on some biological and behavioral parameters of the vector, whereas a second line investigated direct interactions of the phytoplasma with D. maidis during its movement through the vector body following acquisition from plants, and associated microbiota. Indirect effects were investigated in choice experiments in which alighting and oviposition preferences by D. maidis were compared on healthy vs. MBSP-infected plants with variable incubation time (diseased plants with early and advanced symptoms, or still asymptomatic). Likewise, indirect effect of MBSP on the D. maidis biology was determined in two life table experiments in which the vector was reared on healthy vs. MBSP-infected plants expressing advanced disease symptoms or still asymptomatic. Choice experiments showed that alighting and oviposition preferences of D. maidis on MBSP-infected plants compared to healthy plants depend on the pathogen incubation period in the plant. The leafhopper preferred MBSP-infected plants over healthy ones during the asymptomatic phase of the disease, but rejected infected plants with advanced symptoms. The vector was able to acquire MBSP from asymptomatic infected plants shortly (3 days) after inoculation, but transmission efficiency increased when acquisition occurred at later stages of the pathogen incubation period (≥14 days) in the source plants and the test plants showed disease symptoms faster. These results suggest that MBSP modulates D. maidis preference for asymptomatic infected plants in the early stages of the crop, allowing rapid spread of this pathogen. Maize infection by the phytoplasma had a neutral effect on most life table parameters of D. maidis; a lower net reproductivity rate (Ro) was observed in the cohort reared on MBSP-infected plants with advanced symptoms, which was compensated to some extent by a higher sexual ratio. MBSP acquisition by all vector nymphal stadia was confirmed by PCR, and the pathogen as detected in both male and female reproductive organs. Concerning direct MBSP-vector interactions, transmission electron microscopy analyses showed phytoplasma-like cells in the midgut lumen, microvilli and epithelial cells, suggesting that MBSP enters the epithelium midgut through the microvilli wall. Within the epithelial cells, mitochondria and bacteria-like cells (possibly endosymbionts) were observed together with masses of phythoplasma-like cells. In the hemocoel, phytoplasma-like cells grouped into a matrix were also observed in association with bacteria-like cells similar to those observed in the midgut epithelium. Similar associations were found in the salivary gland. Interestingly, in-situ hybridization (FISH) technique revealed a variation in diversity and abundance of the microbiota in intestine and salivary glands of D. maidis adults over time after MBSP acquisition from plants. Sulcia sp., Cardinium sp. and eubacteria increased their abundance over time, whereas Rickettsia sp. decreased. The frequent association of the vector microbiota with the phytoplasma in some tissues of D. maidis suggests that endosymbiotic bacteria may play some role in MBSP-vector interactions.

Degradação anaeróbia de fenol sob diferentes condições nutricionais

A tecnologia anaeróbia tem sido utilizada com sucesso no tratamento de água residuária contendo compostos fenólicos. Recentes pesquisas incluem tais compostos entre aqueles que podem ser degradados através desse processo. O objetivo desse trabalho foi avaliar a degradação do fenol em diferentes condições nutricionais, com ênfase na redução do sulfato. Os experimentos foram realizados com meio de cultura específico para esses microrganismos anaeróbios. Foram realizados ensaios de degradação em reatores em batelada alimentados nas seguintes condições: (1) fenol e sulfato, a diferentes concentrações, com inóculo previamente enriquecido; (2) fenol, sulfato e co-substratos e; (3) fenol, sulfato e extrato de levedura. Todos os ensaios foram realizados em temperatura de 30 graus Celsius, sob agitação de 150 rpm. Foi avaliado o consumo de fenol e sulfato e, produção de metano, em função do tempo, para diferentes concentrações iniciais de fenol e sulfato. Nos ensaios com reatores alimentados com fenol (329,3 mg/l); fenol (307,3 mg/l) e sulfato (160 mg/l); fenol (322.3 mg/l), sulfato (160 mg/l) e lactato (478,16 mg/l); fenol (332,1 mg/l), sulfato (150 mg/l) e etanol (129,76 mg/l), a remoção foi de, respectivamente, 99,8%, 98,2%, 98,8% e 98,8%. Os reatores alimentados com fenol (239,7 mg/l) obtiveram 100% de eficiência na degradação em apenas 11 dias e, os reatores alimentados com fenol (234,3 mg/l) e sulfato (162,5 mg/l) e fenol (256,0 mg/l) e sulfato (500 mg/l) tiveram eficiências de degradação de, respectivamente, 98,8% e 99,3% com 17 dias de operação. Tais eficiências foram obtidas pelo acréscimo de extrato de levedura nos reatores, no início dos ensaios. A caracterização morfológica foi realizada através de microscopia óptica. A diversidade microbiana referente aos Domínios Bacteria e Archaea, além do grupo de bactérias redutoras de sulfato foi avaliada através da técnica de PCR DGGE, onde foram observadas alterações nas populações microbianas, em função das condições nutricionais. Para o Domínio Archaea não foram observadas diferenças nos ensaios realizados. Para o Domínio Bacteria e Grupo das BRS essas diferenças foram, mais facilmente, percebidas com relação ao inóculo e entre os diversos reatores. A alteração na diversidade microbiana pode ter sido decorrente da composição do meio que, nesse caso, foi específico para BRS e a composição do inóculo que continha parte previamente adaptada às BRS. Essas condições adequadas puderam propiciar surgimento e desenvolvimento de populações microbianas capazes de degradar fenol, utilizando sulfato.

Efeito da adição de fibras de cana-de-açúcar pré-tratadas na produção de metano advinda da biodigestão anaeróbia de gorduras do leite

A digestão anaeróbia é uma alternativa para o tratamento de resíduos com altas concentrações de matéria orgânica. Por meio dos processos anaeróbios é possível a produção de biogás, fonte de energia renovável e ambientalmente amigável. Elevadas concentrações de lipídios, todavia, apesar de representarem elevado potencial metanogênico, interferem negativamente nos sistemas de tratamento, podendo inibir a atividade microbiana e, consequentemente, a produção de metano. O presente projeto avaliou o efeito da adição de bagaço de cana-de-açúcar no processo de biodigestão anaeróbia de elevadas concentrações de gorduras advindas de efluentes de laticínio. Para tanto foi utilizado bagaço de cana-de-açúcar in natura e pré-tratadas pelos seguintes métodos: organossolve, hidrotérmico, explosão à vapor e ácido diluído. O uso desse material lignocelulósico teve o objetivo de controlar a inibição causada pelos produtos da hidrólise dos lipídios por meio de sua adsorção e, consequentemente, diminuição das concentrações de tais compostos no meio. Outra hipótese era que o bagaço de cana-de-açúcar pudessem agir como co-substrato no processo de biodigestão anaeróbia. Inicialmente realizaram-se ensaios de biodegradabilidade anaeróbia com concentrações crescentes de gordura, que resultaram em relação entre substrato e microrganismo 0,06, 0,1, 0,2, 0,4 e 0,6 g DQO/gSTV. O ensaio com concentração em que foi verificada a inibição severa (0,4 gDQO/gSTV) do processo foi repetido com adição das fibras tratadas e não tratadas. Aos dados de produção acumulada de metano ajustou-se modelo de Gompertz, e parâmetros cinéticos foram inferidos. O bagaço de cana-de-açúcar mostrou potencial como adsorvente de gordura, pois as produções metanogênicas foram superiores à condição inibida sem adição desse material. A adição de fibras pré-tratadas por método organossolve resultou nas maiores produções de metano.

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota

The mammalian gut microbiota harbors a diverse ecosystem where hundreds of bacterial species interact with each other and their host. Given that bacteria use signals to communicate and regulate group behaviors (quorum sensing), we asked whether such communication between different commensal species can influence the interactions occurring in this environment. We engineered the enteric bacterium, Escherichia coli, to manipulate the levels of the interspecies quorum sensing signal, autoinducer-2 (AI-2), in the mouse intestine and investigated the effect upon antibiotic-induced gut microbiota dysbiosis. E. coli that increased intestinal AI-2 levels altered the composition of the antibiotic-treated gut microbiota, favoring the expansion of the Firmicutes phylum. This significantly increased the Firmicutes/Bacteroidetes ratio, to oppose the strong effect of the antibiotic, which had almost cleared the Firmicutes. This demonstrates that AI-2 levels influence the abundance of the major phyla of the gut microbiota, the balance of which is known to influence human health.

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study.

BACKGROUND Respiratory tract infections and subsequent airway inflammation occur early in the life of infants with cystic fibrosis. However, detailed information about the microbial composition of the respiratory tract in infants with this disorder is scarce. We aimed to undertake longitudinal in-depth characterisation of the upper respiratory tract microbiota in infants with cystic fibrosis during the first year of life. METHODS We did this prospective cohort study at seven cystic fibrosis centres in Switzerland. Between Feb 1, 2011, and May 31, 2014, we enrolled 30 infants with a diagnosis of cystic fibrosis. Microbiota characterisation was done with 16S rRNA gene pyrosequencing and oligotyping of nasal swabs collected every 2 weeks from the infants with cystic fibrosis. We compared these data with data for an age-matched cohort of 47 healthy infants. We additionally investigated the effect of antibiotic treatment on the microbiota of infants with cystic fibrosis. Statistical methods included regression analyses with a multivariable multilevel linear model with random effects to correct for clustering on the individual level. FINDINGS We analysed 461 nasal swabs taken from the infants with cystic fibrosis; the cohort of healthy infants comprised 872 samples. The microbiota of infants with cystic fibrosis differed compositionally from that of healthy infants (p=0·001). This difference was also found in exclusively antibiotic-naive samples (p=0·001). The disordering was mainly, but not solely, due to an overall increase in the mean relative abundance of Staphylococcaceae in infants with cystic fibrosis compared with healthy infants (multivariable linear regression model stratified by age and adjusted for season; second month: coefficient 16·2 [95% CI 0·6-31·9]; p=0·04; third month: 17·9 [3·3-32·5]; p=0·02; fourth month: 21·1 [7·8-34·3]; p=0·002). Oligotyping analysis enabled differentiation between Staphylococcus aureus and coagulase-negative Staphylococci. Whereas the analysis showed a decrease in S aureus at and after antibiotic treatment, coagulase-negative Staphylococci increased. INTERPRETATION Our study describes compositional differences in the microbiota of infants with cystic fibrosis compared with healthy controls, and disordering of the microbiota on antibiotic administration. Besides S aureus, coagulase-negative Staphylococci also contributed to the disordering identified in these infants. These findings are clinically important in view of the crucial role that bacterial pathogens have in the disease progression of cystic fibrosis in early life. Our findings could be used to inform future studies of the effect of antibiotic treatment on the microbiota in infants with cystic fibrosis, and could assist in the prevention of early disease progression in infants with this disorder. FUNDING Swiss National Science Foundation, Fondation Botnar, the Swiss Society for Cystic Fibrosis, and the Swiss Lung Association Bern.

Growth, survival, gene expression, microbiota and tryptic activity during feeding of Scophthalmus maximus first feeding larvae with beta-glucan (MacroGard)

Reflecting the natural biology of mass spawning fish aquaculture production of fish larvae is often hampered by high and unpredictable mortality rates. The present study aimed to enhance larval performance and immunity via the oral administration of an immunomodulator, beta-glucan (MacroGard®) in turbot (Scophthalmus maximus). Rotifers (Brachionus plicatilis) were incubated with or without yeast beta-1,3/1,6-glucan in form of MacroGard® at a concentration of 0.5 g/L. Rotifers were fed to first feeding turbot larvae once a day. From day 13 dph onwards all tanks were additionally fed untreated Artemia sp. nauplii (1 nauplius ml/L). Daily mortality was monitored and larvae were sampled at 11 and 24 dph for expression of 30 genes, trypsin activity and size measurements. Along with the feeding of beta-glucan daily mortality was significantly reduced by ca. 15% and an alteration of the larval microbiota was observed. At 11 dph gene expression of trypsin and chymotrypsin was elevated in the MacroGard® fed fish, which resulted in heightened tryptic enzyme activity. No effect on genes encoding antioxidative proteins was observed, whilst the immune response was clearly modulated by beta-glucan. At 11 dph complement component c3 was elevated whilst cytokines, antimicrobial peptides, toll like receptor 3 and heat shock protein 70 were not affected. At the later time point (24 dph) an anti-inflammatory effect in form of a down-regulation of hsp 70, tnf-alpha and il-1beta was observed. We conclude that the administration of beta-glucan induced an immunomodulatory response and could be used as an effective measure to increase survival in rearing of turbot.

A late Devonian (Frasnian) microbiota from the Farewell-Lyman Hills area, west-central Alaska /

Mode of access: Internet.

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid

This article is protected by copyright. All rights reserved. Acknowledgements: The authors acknowledge support from the Scottish Government Food Land and People programme (RESAS). We would like to thank Lorraine Scobbie and Gary Duncan for technical support. Funding for JP, AWW and 454 pyrosequencing was provided by the Wellcome Trust (grant number 098051).

Infant nutrition and the gut microbiota

Establishment of the intestinal microbiota commences at birth and this colonisation is influenced by a number of factors including mode of delivery, gestational age, mode of feeding, environmental factors and host genetics. As this initial establishment may well influence the health of an individual later in life, it is imperative to understand this process. Therefore, this thesis set out to investigate how early infant nutrition influences the development of a healthy gut microbiota. As part of the INFANTMET project, the intestinal microbiota of 199 breastfed infants was investigated using both culture-dependent and culture-independent approaches. This study revealed that delivery mode and gestational age had a significant impact on early microbial communities. In order to understand host genotype-microbiota interactions, the gut microbiota composition of dichorionic triplets was also investigated. The results suggested that initially host genetics play a significant role in the composition of an individual’s gut microbiota, but by month 12 environmental factors are the major determinant. To investigate the origin of hydrogen sulphide in a case of nondrug- induced sulfhemoglobinemia in a preterm infant, the gut microbiota composition was determined. This analysis revealed the presence of Morganella morganii, a producer of hydrogen sulphide and hemolysins, at a relative abundance 38%, which was not detected in control infants. Following on from this, the negative and short term consequences of intrapartum antibiotic prophylaxis exposure on the early infant intestinal microbiota composition were demonstrated, particularly in breast-fed infants, which are recovered by day 30. Finally, the composition of the breast milk microbiota over the first three months of life was characterised. A core of 12 genera were identified amongst women and the remainder comprised some 195 genera which were individual specific and subject to variations over time. The results presented in this thesis have demonstrated that the development of the infant gut microbiota is complex and highly individual. Clear alterations in the intestinal microbiota establishment process in C-section delivered, preterm and antibiotic exposed infants were shown. Taken together, long-term health benefits for infants, particularly those vulnerable groups, may be conferred through the design of probiotic and prebiotic food ingredients and supplements.

Treatment of Clostridium difficile infection: a national survey of clinician recommendations and the use of faecal microbiota transplantation

Adherence to Clostridium difficile infection treatment guidelines is associated with lower recurrence rates and mortality as well as cost savings. Our survey of Irish clinicians indicates that patients are managed using a variety of approaches. FMT is potentially underutilised despite its recommendation in national and European guidelines.