Characterization of Microbial Communities in Ixodes persulcatus (Ixodida: Ixodidae), a Veterinary and Medical Important Tick Species in Northeastern China

The importance of ticks in veterinary and medical science has received much attention. The dominant tick species in northeastern China, Ixodes persulcatus tick can transmit various pathogens to humans and animals and there are some studies on the microbiome composition of this tick. Our study characterized the bacterial communities in I. persulcatus by 16S amplicon pyrosequencing and described the differences of microorganisms in male and female tick and assessed the variation of microorganisms in the development stages in northeastern China. We mainly found the following bacteria genera: Pseudomonas (Pseudomonadales: Pseudomonadaceae), Citrobacter (Enterobacteriales: Enterobacteriaceae), and Rickettsia (Rickettsiales: Rickettsiaceae). Rickettsia is common and harmful pathogen transmitted by ticks. Meanwhile, we found there were differences between male and female tick of microbiomes, and the diversity of microbiome increased from engorged female ticks to eggs, but decreased when the eggs were molting into larvae. Our data showed that male ticks exhibited greater microbial diversity than female I. persulcatus tick and larvae presented with a different bacterial community compared to engorged female tick and hatched eggs. These findings may be useful for further understanding the interaction between I. persulcatus and microbiome biology.

PSIX-2 Potential role of rumen microbiota in altering average daily gain and feed efficiency in meat goats fed simple and mixed pastures using bacterial tag-encoded FLX amplicon pyrosequencing

Our objective was to examine whether the comparative abundance of the Bacteroidetes (B) and Firmicutes (F) bacterial phyla in meat goats fed simple and mixed forages influenced average daily gain (ADG), rumen fermentation parameters and bacterial diversity changes using a tag-encoded FLX amplicon pyrosequencing (bTEFAP). Thirty-six Kiko-cross growing meat goats (BW = 27.7 ± 2.83) at approximate age of 7 mo were used in this study. Animals were randomly allocated to three pasture treatment groups (n = 12) as follows: (1) bermudagrass (BG; Cynodon dactylon), (2) sun hemp (SH; Crotalaria juncea) forage, and (3) BG + SH forage combinations for 45-d. Results indicated that there were no differences in initial BW among treatments, but final BW and ADG were higher (P < 0.01) for SH and BG + SH combinations than for BG alone. We investigated the alterations between the different forage diets and found that ADG and rumen fermentation (A/P ratio), were highly correlated with the abundance of various bacterial populations within the rumen microbiome. There were linear decreases in percentage of Bacteroidetes (R2 = -0.84; P < 0.05) associated with decreasing ADG. In contrast, increased ADG was linearly associated with higher percentages of Firmicutes (R2 = 0.79; P < 0.05), F/B ratio (R2 = 0.88; P = 0.07), total VFA (R2 = 0.45; P < 0.05), and lower A/P ratio (R2 = -0.72; P < 0.01). This suggest that the substrate and bacterial community have the role in adapting host biological parameters in meat goats. The abundance examination of both Bacteroidetes and Firmicutes will be useful for exploring the structure of gut microbiota as an estimate of animal performance.

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability

The access and recycling of the base cations are essential processes for the long-lasting functioning of forest ecosystems. While the role of soil bacterial communities has been demonstrated in mineral weathering and tree nutrition, our understanding of the link between the availability of base cations and the functioning of these communities remains limited. To fill this gap, we developed a microcosm approach to investigate how an increase in key base cations (potassium or magnesium) impacted the taxonomic and functional structures of the bacterial communities. During a 2-month period after fertilization with available potassium or magnesium, soil properties, global functions (metabolic potentials and respiration) as well as mineral weathering bioassays and 16S rRNA amplicon pyrosequencing were monitored. Our analyses showed no or small variations in the taxonomic structure, total densities and global functions between the treatments. In contrast, a decrease in the frequency and effectiveness of mineral weathering bacteria was observed in the fertilized treatments. Notably, quantitative PCR targeting specific genera known for their mineral weathering ability (i.e., Burkholderia and Collimonas) confirmed this decrease. These new results suggest that K and Mg cation availability drives the distribution of the mineral weathering bacterial communities in forest soil.

Microbial Community of Saline, Alkaline Lakes in the Nebraska Sandhills Based on 16S rRNA Gene Amplicon Sequence Data

The Nebraska Sandhills region contains over 1,500 geochemically diverse interdunal lakes, some of which are potassium rich, alkaline, and hypersaline. Here, we report 16S rRNA amplicon pyrosequencing data on the water and sediment microbial communities of eight alkaline lakes in the Sandhills of western Nebraska.

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals

Directed modulation of the colonic bacteria to metabolize lactose effectively is a potentially useful approach to improve lactose digestion and tolerance. A randomized, double-blind, multisite placebo-controlled trial conducted in human subjects demonstrated that administration of a highly purified (>95%) short-chain galactooligosaccharide (GOS), designated “RP-G28,” significantly improved clinical outcomes for lactose digestion and tolerance. In these individuals, stool samples were collected pretreatment (day 0), after GOS treatment (day 36), and 30 d after GOS feeding stopped and consumption of dairy products was encouraged (day 66). In this study, changes in the fecal microbiome were investigated using 16S rRNA amplicon pyrosequencing and high-throughput quantitative PCR. At day 36, bifidobacterial populations were increased in 27 of 30 of GOS subjects (90%), demonstrating a bifidogenic response in vivo. Relative abundance of lactose-fermenting Bifidobacterium, Faecalibacterium, and Lactobacillus were significantly increased in response to GOS. When dairy was introduced into the diet, lactose-fermenting Roseburia species increased from day 36 to day 66. The results indicated a definitive change in the fecal microbiome of lactose-intolerant individuals, increasing the abundance of lactose-metabolizing bacteria that were responsive to dietary adaptation to GOS. This change correlated with clinical outcomes of improved lactose tolerance.

Microbial Communities in Globodera pallida Females Raised in Potato Monoculture Soil

Globodera spp. are under strict quarantine in many countries. Suppressiveness to cyst nematodes can evolve under monoculture of susceptible hosts. Females developing in potato monoculture soil infested with G. pallida populations Chavornay or Delmsen were examined for inherent microbial communities. In the greenhouse, nonheated and heat-treated (134°C for 10 min) portions of this soil were placed in root observation chambers, planted with Solanum tuberosum ‘Selma’, and inoculated with G. pallida Pa3 Chavornay. At harvest in Delmsen soil, cysts had fewer eggs in nonheated than heat-treated soil. In denaturing gradient gel electrophoresis analysis, bacterial and fungal fingerprints were characterized by a high variability between replicates; nonheated soils displayed more dominant bands than heated soils, indicating more bacterial and fungal populations. In amplicon pyrosequencing, females from nonheated portions frequently contained internal transcribed spacer sequences of the fungus Malassezia. Specific for the Chavornay and Delmsen population, ribosomal sequences of the bacteria Burkolderia and Ralstonia were abundant on eggs. In this first report of microbial communities in G. pallida raised in potato monoculture, candidate microorganisms perhaps associated with the health status of the eggs of G. pallida were identified. If pathologies on cyst nematodes can be ascertained, these organisms could improve the sustainability of production systems.

Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha)

Indigenous beers (chicha) are part of the indigenous culture in Ecuador. The fermentation process of these beers probably relies on microorganisms from fermented substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava) using bacterial culture and 16S ribosomal RNA (rRNA) gene-based tag-encoded FLX amplicon pyrosequencing (bTEFAP). Surprisingly, we found thatStreptococcus salivariusandStreptococcus mutans(part of the human oral microbiota) were among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated thatS. salivariusandS. mutans(isolated from these beers) could proliferate in cassava mush.Lactobacillussp. was predominantly present in most types of Ecuadorianchicha.

Domestic shower hose biofilms contain fungal species capable of causing opportunistic infection

The domestic environment can be a source of pathogenic bacteria. We show here that domestic shower hoses may harbour potentially pathogenic bacteria and fungi. Well-developed biofilms were physically removed from the internal surface of shower hoses collected in four locations in England and Scotland. Amplicon pyrosequencing of 16S and 18S rRNA targets revealed the presence of common aquatic and environmental bacteria, including members of the Actinobacteria, Alphaproteobacteria, Bacteroidetes and non-tuberculous Mycobacteria. These bacteria are associated with infections in immunocompromised hosts and are widely reported in shower systems and as causes of water-acquired infection. More importantly, this study represents the first detailed analysis of fungal populations in shower systems and revealed the presence of sequences related to Exophiala mesophila, Fusarium fujikuroi and Malassezia restricta. These organisms can be associated with the environment and healthy skin, but also with infection in compromised and immuno-competent hosts and occurrence of dandruff. Domestic showering may result in exposure to aerosols of bacteria and fungi that are potentially pathogenic and toxigenic. It may be prudent to limit development of these biofilms by the use of disinfectants, or regular replacement of hoses, where immuno-compromised persons are present.