Effect of inclusion of lactulose and Lactobacillus plantarum on the intestinal environment and performance of piglets at weaning

The prebiotic lactulose, a probiotic strain of Lactobacillus plantarum (L. plantarum) and a synbiotic combination of these two agents were evaluated as growth promoters in 25–39-day old commercial weaning pigs. Ninety-six weaning pigs were allocated into 32 pens, taking initial weight into account, and distributed into four groups as follows: a control diet (CTR), the same diet supplemented daily with L. plantarum (109 CFU/mL sprayed on top; 20 mL/pig) (LPN); 10 g/kg lactulose (LAC) or a combination of both treatments (SYN). At day 14, eight piglets from each group were euthanized and proximal colon digesta was sampled for luminal pH, short-chain fatty acids (SCFA) and lactic acid concentrations. Deoxyribonucleic acid was extracted from colonic digesta and the microbial community was profiled by terminal restriction fragment length polymorphism analysis (T-RFLP) and qPCR. Blood urea nitrogen (BUN) and acute-phase proteins (Pig-MAP) were measured. Lactulose treatment (LAC) improved feed intake (P<0.05), average daily gain (P<0.01), feed:gain ratio (P<0.05) and reduced BUN (P<0.01). Both, LAC and LPN treatment, decreased the Enterobacteriaceae:Lactobacillus spp. ratio in the colonic luminal contents (P<0.05). Moreover LPN treatment promoted a decrease in the percentage of branched fatty acids (P<0.01) suggesting a reduction in proteolytic microbial activity. Microbial profiling of colonic luminal contents by T-RFLP revealed changes in some microbial species. Terminal restriction fragments (TRFs) compatible with Bifidobacterium thermoacidophilum were more frequently detected in experimental diets compared to CTR (P<0.05). Pigs receiving SYN diet demonstrated the combined positive effects of individual LAC and LPN treatment although we were not able to show a specific increase in the probiotic strain with the inclusion of lactulose. Collectively, these data suggest the combination of lactulose and L. plantarum acts as a complementary synbiotic, but not as a synergistic combination.

Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota

The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified Clostridiales, Bacteroidaceae, and Lactobacillaceae species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to Lactobacillus spp., 155 belonged to Clostridium spp., and 66 belonged to Streptococcus spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.

Comparative analysis of intestinal tract models

The human gut is a complex ecosystem occupied by a diverse microbial community. Modulation of this microbiota impacts health and disease. The definitive way to investigate the impact of dietary intervention on the gut microbiota is a human trial. However, human trials are expensive and can be difficult to control; thus, initial screening is desirable. Utilization of a range of in vitro and in vivo models means that useful information can be gathered prior to the necessity for human intervention. This review discusses the benefits and limitations of these approaches.

Cadaver decomposition in terrestrial ecosystems

A dead mammal (i.e. cadaver) is a high quality resource (narrow carbon:nitrogen ratio, high water content) that releases an intense, localised pulse of carbon and nutrients into the soil upon decomposition. Despite the fact that as much as 5,000 kg of cadaver can be introduced to a square kilometre of terrestrial ecosystem each year, cadaver decomposition remains a neglected microsere. Here we review the processes associated with the introduction of cadaver-derived carbon and nutrients into soil from forensic and ecological settings to show that cadaver decomposition can have a greater, albeit localised, effect on belowground ecology than plant and faecal resources. Cadaveric materials are rapidly introduced to belowground floral and faunal communities, which results in the formation of a highly concentrated island of fertility, or cadaver decomposition island (CDI). CDIs are associated with increased soil microbial biomass, microbial activity (C mineralisation) and nematode abundance. Each CDI is an ephemeral natural disturbance that, in addition to releasing energy and nutrients to the wider ecosystem, acts as a hub by receiving these materials in the form of dead insects, exuvia and puparia, faecal matter (from scavengers, grazers and predators) and feathers (from avian scavengers and predators). As such, CDIs contribute to landscape heterogeneity. Furthermore, CDIs are a specialised habitat for a number of flies, beetles and pioneer vegetation, which enhances biodiversity in terrestrial ecosystems.

The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons

Despite the accumulating knowledge on the development and establishment of the gut microbiota, its role as a reservoir for multidrug resistance is not well understood. This study investigated the prevalence and persistence patterns of an integrase gene (int1), used as a proxy for integrons (which often carry multiple antimicrobial resistance genes), in the fecal microbiota of 147 mothers and their children sampled longitudinally from birth to 2 years. The study showed the int1 gene was detected in 15% of the study population, and apparently more persistent than the microbial community structure itself. We found int1 to be persistent throughout the first two years of life, as well as between mothers and their 2-year-old children. Metagenome sequencing revealed integrons in the gut meta-mobilome that were associated with plasmids and multidrug resistance. In conclusion, the persistent nature of integrons in the infant gut microbiota makes it a potential reservoir of mobile multidrug resistance.

Host and habitat filtering in seedling root-associated fungal communities: taxonomic and functional diversity are altered in ‘novel’ soils

Climatic and land use changes have significant consequences for the distribution of tree species, both through natural dispersal processes and following management prescriptions. Responses to these changes will be expressed most strongly in seedlings near current species range boundaries. In northern temperate forest ecosystems, where changes are already being observed, ectomycorrhizal fungi contribute significantly to successful tree establishment. We hypothesised that communities of fungal symbionts might therefore play a role in facilitating, or limiting, host seedling range expansion. To test this hypothesis, ectomycorrhizal communities of interior Douglas-fir and interior lodgepole pine seedlings were analysed in a common greenhouse environment following growth in five soils collected along an ecosystem gradient. Currently, Douglas-fir’s natural distribution encompasses three of the five soils, whereas lodgepole pine’s extends much further north. Host filtering was evident amongst the 29 fungal species encountered: 7 were shared, 9 exclusive to Douglas-fir and 13 exclusive to lodgepole pine. Seedlings of both host species formed symbioses with each soil fungal community, thus Douglas-fir did so even where those soils came from outside its current distribution. However, these latter communities displayed significant taxonomic and functional differences to those found within the host distribution, indicative of habitat filtering. In contrast, lodgepole pine fungal communities displayed high functional similarity across the soil gradient. Taxonomic and/or functional shifts in Douglas-fir fungal communities may prove ecologically significant during the predicted northward migration of this species; especially in combination with changes in climate and management operations, such as seed transfer across geographical regions for forestry purposes.

DGGE with genomic DNA: Suitable for detection of numerically important organisms but not for identification of the most abundant organisms

Identification of all important community members as well as of the numerically dominant members of a community are key aspects of microbial community analysis of bioreactor samples. A systematic study was conducted with artificial consortia to test whether denaturing gradient gel electrophoresis (DGCE) is a reliable technique to obtain such community data under conditions where results would not be affected by differences in DNA extraction efficiency from cells. A total of 27 consortia were established by mixing DNA extracted from Escherichia coli K12, Burkholderia cepacia and Stenotrophomonas maltophilia in different proportions. Concentrations of DNA of single organisms in the consortia were either 0.04, 0.4 or 4 ng/mu l. DGGE-PCR of genomic DNA with primer sets targeted at the V3 and V6-V8 regions of the 16S rDNA failed to detect the three community members in only 7% of consortia, but provided incorrect information about dominance or co-dominance for 85% and 89% of consortia with the primer sets for the V6-V8 and V3 regions, respectively. The high failure rate in detection of dominant B. cepacia with the primers for the V6-V8 region was attributable to a single nucleoticle primer mismatch in the target sequences of both, the forward and reverse primer. Amplification bias in PCR of E. coli and S. maltophilia for the V6-V8 region and for all three organisms for the V3 region occurred due to interference of genomic DNA in PCR-DGGE, since a nested PCR approach, where PCR-DGGE was started from mixtures of 16S rRNA genes of the organisms, provided correct information about the relative abundance of original DNA in the sample. Multiple bands were not observed in pure culture amplicons produced with the V6-V8 primer pair, but pure culture V3 DGGE profiles of E. coli, S. maltophilia and B. cepacia contained 5, 3 and 3 bands, respectively. These results demonstrate DGGE was suitable for identification of all important community members in the three-membered artificial consortium, but not for identification of the dominant organisms in this small community. Multiple DGGE bands obtained for single organisms with the V3 primer pair could greatly confound interpretation of DGGE profiles. (C) 2008 Elsevier Ltd. All rights reserved.

Chemical variability within the marine sponge Aplysina fulva

Dibromotyrosine-derived metabolites are of common occurrence within marine sponges belonging to the order Verongida. However, previous chemical analysis of crude extracts obtained from samples of the verongid sponge Aplysina fulva collected in Brazil did not provide any dibromotyrosine-derived compounds. In this investigation, five samples of A. fulva from five different locations along the Brazilian coastline and one sample from a temperate reef in the South Atlantic Bight (SAB) (Georgia, USA) were investigated for the presence of bromotyrosine-derived compounds. All six samples collected yielded dibromotyrosine-derived compounds, including a new derivative, named aplysinafulvin, which has been identified by. analysis of spectroscopic data. These results confirm previous assumptions that dibromotyrosine-derived metabolites can be considered as chemotaxonomic markers of verongid sponges. The isolation of aplysinafulvin provides additional support for a biogenetic pathway involving an arene oxide intermediate in the biosynthesis of Verongida metabolites. It cannot yet be established if the chemical variability observed among the six samples of A.fulva collected in Brazil and the SAB is the result of different environmental factors, distinct chemical extraction and isolation protocols, or a consequence of hidden genetic diversity within the postulated morphological plasticity of this species. (C) 2007 Elsevier Ltd. All rights reserved.

Atividade microbiana do solo em pomar de laranja em resposta ao cultivo de adubos verdes

Adubos verdes (AVs) são condicionadores do solo utilizados para a melhoria da estrutura e fertilidade do solo. Este estudo avaliou o efeito de Crotalaria spectabilis Roth (crotalária), Cajanus cajan (L) Millsp (guandu) e Brachiaria decumbens Stapf (braquiária) nas propriedades microbiológicas e bioquímicas do solo sob laranjal. As leguminosas foram plantadas nas entrelinhas do laranjal e, após 3 meses, cortadas e lançadas nas entrelinhas. A braquiária, já estabelecida, foi roçada e lançada nas entrelinhas. Após 5 meses, as amostras de solo foram coletadas na entrelinha e na linha, na profundidade de 0-20 cm. O delineamento experimental foi em parcela subdividida. Efeito significativo (p< 0,05%) da aplicação dos AV sobre as contagens de bactérias, as atividades da desidrogenase e nitrificante foram obtidas e aumentaram, em média, de 20, 39 e 190%, respectivamente. O número de fungos diminuiu de 57%. A atividade da urease e a solubilizadora, e os conteúdos de matéria orgânica e umidade não foram influenciados pela aplicação dos AVs. Dentre as plantas, respostas significativas foram obtidas decorrentes do estímulo da atividade da desidrogenase em 57% pelo guandu, da urease em 58% pela braquiária, solubilizadora em 346% pela crotalária e nitrificante em 236% pelo guandu ou braquiária em relação aos demais AVs. Estes resultados sugerem que a aplicação de AVs durante anos consecutivos pode estimular a ação dos microrganismos e melhorar a qualidade do solo.

Disponibilidade de nutrientes no solo: decomposição e liberação de compostos orgânicos de resíduos vegetais

O objetivo principal desta revisão foi reunir informações a respeito da ação de compostos orgânicos produzidos por plantas na disponibilidade de nutrientes nos solos, principalmente sobre os cátions Ca, Mg e K e sobre o ânion fosfato. O sistema de cultivo adotado ocasiona mudanças nas propriedades químicas e físicas do solo, especialmente na disponibilidade de nutrientes e condicionamento físico do solo. Tem-se observado o acúmulo de nutrientes nas camadas superficiais do solo no sistema de semeadura direta, pelo não-revolvimento do solo e pela deposição de resíduos de culturas na superfície. Os ácidos orgânicos provenientes de plantas podem interagir com a fase sólida e ocupar os sítios de adsorção de nutrientes, competindo diretamente com eles e aumentando sua disponibilidade no solo. A adição de resíduos vegetais pode promover, antes da humificação, a elevação do pH, por promover complexação de H e Al com compostos do resíduo vegetal, deixando Ca, Mg e K mais livres em solução, o que pode ocasionar aumento na saturação da CTC por estes cátions de reação básica. Também é normal observar o aumento na disponibilidade de P no solo com a adição de resíduos vegetais, tanto pelo P presente no resíduo como por competição de compostos orgânicos dos resíduos pelos sítios de troca no solo. A persistência dos compostos orgânicos também é fator que tem grande interferência nos processos de sorção/dessorção de cátions e ânions, dependendo da atividade microbiana, da disponibilidade metabólica do substrato carbonado e da sorção aos colóides do solo.

Resíduos orgânicos como recondicionante de subsolo degradado e efeitos na atividade microbiana e fertilidade em cultivo de barbatimão

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Antagonistic interactions between garden yeasts and microfungal garden pathogens of leaf-cutting ants

We investigate the diversity of yeasts isolated in gardens of the leafcutter ant Atta texana. Repeated sampling of gardens from four nests over a 1-year time period showed that gardens contain a diverse assemblage of yeasts. The yeast community in gardens consisted mostly of yeasts associated with plants or soil, but community composition changed between sampling periods. In order to understand the potential disease-suppressing roles of the garden yeasts, we screened isolates for antagonistic effects against known microfungal garden contaminants. In vitro assays revealed that yeasts inhibited the mycelial growth of two strains of Escovopsis (a specialized attine garden parasite), Syncephalastrum racemosum (a fungus often growing in gardens of leafcutter lab nests), and the insect pathogen Beauveria bassiana. These garden yeasts add to the growing list of disease-suppressing microbes in attine nests that may contribute synergistically, together with actinomycetes and Burkholderia bacteria, to protect the gardens and the ants against diseases. Additionally, we suggest that garden immunity against problem fungi may therefore derive not only from the presence of disease-suppressing Pseudonocardia actinomycetes, but from an enrichment of multiple disease-suppressing microorganisms in the garden matrix.

Determinação de fósforo microbiano: comparação entre métodos e coberturas florestais

Muitos trabalhos mostram a importância da biomassa microbiana do solo (BMS), principalmente como fonte/dreno de C e de N em plantações florestais; contudo, são escassos os trabalhos relacionados ao fósforo microbiano (PBM), sobretudo aqueles relativos aos métodos de determinação do PBM nesses ecossistemas. O presente trabalho foi realizado com o objetivo de avaliar métodos de determinação do PBM em solo com diferentes coberturas vegetais. O trabalho consistiu da análise de amostras de Latossolo Vermelho-Amarelo distrófico muito argiloso (LVAd) localizado no município de Viçosa (MG), coletadas nas profundidades de 0 a 5 e 5 a 10 cm, em áreas com as seguintes coberturas vegetais: pínus (Pinus taeda), eucalipto (Eucalyptus grandis) e floresta nativa. Para determinação do P microbiano, foram empregados os métodos fumigação-extração (FE), irradiação com micro-ondas-extração (IE) e irradiação com micro-ondas-extração com membrana de troca aniônica (EMTA). em termos gerais, menores teores de PBM foram obtidos com o método irradiação-extração. Considerando a cobertura vegetal, foi detectada diferença significativa entre os três métodos sob floresta de eucalipto e floresta nativa, principalmente na camada superficial. Sob pínus, apenas o método IE diferiu dos demais, na camada subsuperficial. Menores coeficientes de variação (CV) foram obtidos com o FE, retratando maior precisão do método. Entretanto, o método IE mostrou-se, em termos operacionais, o mais adequado à determinação do PBM quando se tem maior número de amostras. Com relação às coberturas vegetais, a grande variabilidade observada nos CVs obtidos para cada cobertura, nos três métodos testados, inviabiliza a escolha de um único método que apresente maior precisão na avaliação do PBM.

Efeito do sistema de plantio e doses do nicosulfuron sobre a atividade microbiana do solo

Objetivou-se com este trabalho avaliar o efeito do atrazine em mistura com nicosulfuron sobre a atividade microbiológica do solo em sistema de cultivo convencional ou semeadura direta. O estudo foi realizado em área de integração milho-braquiária, sendo feitas aplicações dos herbicidas atrazine + nicosulfuron em duas dosagens (1.500 + 10 e 1.500 + 30 g h-1) e mantidas duas áreas testemunhas: não capinada e capinada sem cultivo. Por ocasião do florescimento, foram retiradas amostras do solo em cada unidade experimental, para determinação da taxa de desprendimento de CO2, carbono da biomassa microbiana (CBM) e quociente metabólico (qCO2). Entre os sistemas de cultivo, a taxa de desprendimento de CO2 foi menor nas parcelas não capinadas. O CBM foi maior no sistema de plantio direto, sendo afetado negativamente pela ausência de vegetação. Menores valores para CBM foram observados nas amostras de solo das parcelas capinadas. Os maiores valores de qCO2 foram observados no sistema convencional. No sistema de plantio direto não se verificou diferença entre os tratamentos cujo solo recebeu herbicida e o isento de capinas. Dessa forma, pode-se concluir que os indicadores microbiológicos avaliados foram sensíveis aos tratamentos propostos, indicando menor distúrbio ao solo quando em sistema de semeadura direta. Entretanto, na integração lavoura-pecuária em sistema convencional de cultivo, o efeito negativo dos herbicidas é aumentado com o incremento na dose do nicosulfuron.

Atividade rizosférica de solo tratado com herbicida durante processo de remediação por Stizolobium aterrimum

This study aimed to evaluate the soil microbiota activity associated to S. aterrimum rhizosphere, during the phytoremediation process of a soil contaminated with trifloxysulfuron-sodium. S. aterrimum was cultivated in vases (6, 0 L) filled with soil, after trifloxysulfuron-sodium, at 7.5 g ha -1, was applied or not. Every 15 days after sowing (DAS), rhizospheric soil was collected for soil microbial respiration (amount of evolved CO 2) and microbial biomass carbon (MBC) analysis. To determine herbicide residues in the soil samples, after phytoremediation, Sorghum bicolor L. was cultivated as an indicator species, in addition to high performance liquid chromatography (HPLC) analysis. The microbiota associated to S. aterrimum rhizosphere showed to be sensitive to trifloxysulfuron-sodium and may be used as a microbiological indicator of disturbances caused by this herbicide in the environment. Regarding time for remediation, 45 days of development is enough for S. aterrimum to reduce residual trifloxysulfuron- sodium to a level not able to cause toxicity to the indicator plant.