The chigger microbiome: big questions in a tiny world

‘Chiggers’ (trombiculid mite larvae) are best known as vectors of rickettsial pathogens, Orientia spp., which cause a zoonosis, scrub typhus. However, several other pathogens (e.g., Hantaan orthohantavirus, Dabie bandavirus, Anaplasma spp., Bartonella spp., Borrelia spp., and Rickettsia spp.) and bacterial symbionts (e.g., Cardinium, Rickettsiella, and Wolbachia) are being reported from chiggers with increasing frequency. Here, we explore the surprisingly diverse chigger microbiota and potential interactions within this microcosm. Key conclusions include a possible role for chiggers as vectors of viral diseases; the dominance in some chigger populations of unidentified symbionts in several bacterial families; and increasing evidence for vertical transmission of potential pathogens and symbiotic bacteria in chiggers, suggesting intimate interactions and not simply incidental acquisition of bacteria from the environment or host.     

Horizontal transfer of antibiotic resistance genes in a membrane bioreactor

Growing attention has been paid to the dissemination of antibiotic resistance genes (ARGs) in wastewater microbial communities. The application of membrane bioreactors (MBRs) in wastewater treatment is becoming increasingly widespread. We hypothesized that the transfer of ARGs among bacteria could occur in MBRs, which combine a high density of bacterial cells, biofilms, and antibiotic resistance bacteria or ARGs. In this study, the transfer discipline and dissemination of the RP4 plasmid in MBRs were investigated by the counting plate method, the MIDI microorganism identification system, and quantitative polymerase chain reaction (qPCR) techniques. The results showed that the average transfer frequency of the RP4 plasmid from the donor strain to cultivable bacteria in activated sludge was 2.76 × 10⁻⁵ per recipient, which was greater than the transfer frequency in wastewater and bacterial sludge reported previously. In addition, many bacterial species in the activated sludge had received RP4 by horizontal transfer, while the genera of Shewanella spp., Photobacterium spp., Pseudomonas spp., Proteus spp., and Vibrio spp. were more likely to acquire this plasmid. Interestingly, the abundance of the RP4 plasmid in total DNA remained at high levels and relatively stable at 10⁴ copies/mg of biosolids, suggesting that ARGs were transferred from donor strains to activated sludge bacteria in our study. Thus, the presence of ARGs in sewage sludge poses a potential health threat.     

Efficacy of some commerical disinfectants against the bacterial isolates from a poultry slaughterhouse in Turkey

In this study, efficacy of seven different commercial disinfectant preparations was investigated against characteristic bacteria of a poultry slaughterhouse in Ankara (Turkey) by using paper disc-agar diffusion method and surface effectiveness test. According to paper disc-agar diffusion method, some disinfectants had wide efficacy against the test bacteria. The disinfectant effectiveness generally increased by the increasing of disinfectant concentration. However, some disinfectants were ineffective even though at their highest concentrations. The most effective disinfectant was B which contains QAC as active agent.Staphylococcus spp.,Staphyloccus aureus andEscherichia coli were the most sensitive bacteria to the disinfectants. Some pathogenic isolates, especiallySalmonella spp. andCampylobacter spp., were the most resistant ones to many of the disinfectants tested. The results of paper disc-agar diffusion method indicated the importance of characteristic bacterial strains of food plants as the test bacteria for disinfectant efficacy tests. Conversely of paper disc-agar diffusion method, all disinfectants were effective against the isolates by surface effectiveness test depending on exposure time. The disinfectants, except A and F, produced at least 3 log unit reduction during 5 min of exposure. However, all disinfectants at their lowest concentrations were effective against all tested bacteria during 15 and 30 min by this test.     

Qualitative microbiological changes during decomposition of plant material in a sandy sierozem soil

The successive qualitative microbial changes during the decomposition of bajra stalk in a sandy sierozem soil were studied.Alternaria spp.,Aspergillus spp.,Cladosporium spp.,Fusarium spp.Gliocladium spp.,Mucor spp. andRhizopus spp. were most common fungi. The bacteria observed wereAchromobacter, Arthrobacter, Bacillus, Micrococcus, Pseudomonas andXanthomonas. Cellvibrio andCellulomonas were also observed.     

Bacterial communities of some brown and red algae from Peter the Great Bay, the Sea of Japan

The structure of microbial communities of brown algae, red algae, and of the red alga Gracilaria verrucosa, healthy and affected with thallus rot, were comparatively investigated; 61 strains of heterotrophic bacteria were isolated and characterized. Most of them were identified to the genus level, some Vibrio spp., to the species level according to their phenotypic properties and the fatty acid composition of cellular lipids. The composition of the microflora of two species of brown algae was different. In Chordaria flagelliphormis, Pseudomonas spp. prevailed, and in Desmarestia viridis, Bacillus spp. The composition of the microflora of two red algae, G. verrucosa and Camphylaephora hyphaeoides, differed mainly in the ratio of prevailing groups of bacteria. The most abundant were bacteria of the CFB cluster and pseudoalteromonads. In addition, the following bacteria were found on the surface of the algae: Sulfitobacter spp., Halomonas spp., Acinetobacter sp., Planococcus sp., Arthrobacter sp., and Agromyces sp. From tissues of the affected G. verrucosa, only vibrios were isolated, both agarolytic and nonagarolytic. The existence of specific bacterial communities characteristic of different species of algae is suggested and the relation of Vibrio sp. to the pathological process in the tissues of G. verrucosa is supposed.     

Simultaneous and rapid detection of enteric pathogens from raw milk by multiplex PCR

Enteroinvasive Escherichia coli (EIEC), heat-labile enterotoxin (LT) E. coli, Shigella spp., and Salmonella spp. are common enteric pathogens, which cause food-borne diseases if consumed in contaminated milk products. The rapid and reliable methods for detecting are imperative for reduction in hazard of infection. In this study, we selected primers, optimized the polymerase chain reaction (PCR) conditions, and analyzed the sensitivity and specificity of the multiplex PCR assay to screen raw milk from these enteric bacteria. Furthermore, EIEC, LT-E. coli, Shigella spp., Salmonella spp., and 11 non-targeted pathogenic strains were performed for the specificity of the multiplex PCR. Specific bands showed in EIEC, LT-E. coli, Shigella spp., and Salmonella spp. but no bands showed in other 11 pathogenic strains. The sensitivity of multiplex PCR was relatively high, was rounded to 200 CFU/ml (Shigella spp. and EIEC), 320 CFU/ml (Salmonella spp.), and 100 CFU/ml (LT-E. coli). This method for simultaneous and rapid detection of enteric pathogens (EIEC, LT-E. coli, Shigella spp., and Salmonella spp.) in raw milk showed high sensitivity and specificity, and led to faster track to report results.     

Diversity of sporadic symbionts and nonsymbiotic endophytic bacteria isolated from nodules of woody, shrub, and food legumes in Ethiopia

Fifty-five bacterial isolates were obtained from surface-sterilized nodules of woody and shrub legumes growing in Ethiopia: Crotalaria spp., Indigofera spp., and Erythrina brucei, and the food legumes soybean and common bean. Based on partial 16S rRNA gene sequence analysis, the majority of the isolates were identified as Gram-negative bacteria belonging to the genera Achromobacter, Agrobacterium, Burkholderia, Cronobacter, Enterobacter, Mesorhizobium, Novosphingobium, Pantoea, Pseudomonas, Rahnella, Rhizobium, Serratia, and Variovorax. Seven isolates were Gram-positive bacteria belonging to the genera Bacillus, Paenibacillus, Planomicrobium, and Rhodococcus. Amplified fragment length polymorphism (AFLP) fingerprinting showed that each strain was genetically distinct. According to phylogenetic analysis of recA, glnII, rpoB, and 16S rRNA gene sequences, Rhizobium, Mesorhizobium, and Agrobacterium were further classified into six different genospecies: Agrobacterium spp., Agrobacterium radiobacter, Rhizobium sp., Rhizobium phaseoli, Mesorhizobium sp., and putative new Rhizobium species. The strains from R. phaseoli, Rhizobium sp. IAR30, and Mesorhizobium sp. ERR6 induced nodules on their host plants. The other strains did not form nodules on their original host. Nine endophytic bacterial strains representing seven genera, Agrobacterium, Burkholderia, Paenibacillus, Pantoea, Pseudomonas, Rhizobium, and Serratia, were found to colonize nodules of Crotalaria incana and common bean on co-inoculation with symbiotic rhizobia. Four endophytic Rhizobium and two Agrobacterium strains had identical nifH gene sequences with symbiotic Rhizobium strains, suggesting horizontal gene transfer. Most symbiotic and nonsymbiotic endophytic bacteria showed plant growth-promoting properties in vitro, which indicate their potential role in the promotion of plant growth when colonizing plant roots and the rhizosphere.     

Migratory birds travelling to Bangladesh are potential carriers of multi-drug resistant Enterococcus spp., Salmonella spp., and Vibrio spp.

Antimicrobial resistance (AMR) is a major health crisis globally. Migratory birds could be a potential source for antibiotic resistant (ABR) bacteria. Not much is known about their role in the transmission of ABR in Bangladesh. In this study, a total of 66 freshly dropped fecal materials of migratory birds were analyzed. Bacterial isolation and identification were based on cultural properties, biochemical tests, and polymerase chain reaction (PCR). The disk diffusion method was employed to evaluate antibiogram profiles. By PCR, out of 66 samples, the detection rate of Enterococcus spp. (60.61%; 95% confidence interval: 48.55–71.50%) was found significantly higher than Salmonella spp. (21.21%; 95% CI: 13.08–32.51%) and Vibrio spp. (39.40%; 95% CI: 28.50–51.45%). Enterococcus isolates were frequently found resistant (100–40%) to ampicillin, streptomycin, meropenem, erythromycin, and gentamicin; Salmonella isolates were frequently resistant (72–43%) to chloramphenicol, tetracycline, ampicillin, streptomycin, and erythromycin; and Vibrio spp. isolates were frequently resistant (77–31%) to vancomycin, ampicillin, erythromycin, tetracycline, and streptomycin. In addition, 60% (95% CI: 44.60–73.65%) Enterococcus spp., 85.71% (95% CI: 60.06–97.46%) Salmonella spp., and 76.92% (95% CI: 57.95–88.97%) Vibrio spp. isolates were multi-drug resistant (MDR) in nature. Three isolates (one from each bacterium) were found resistant against six classes of antibiotics. The bivariate analysis revealed strong associations (both positive and negative) between several antibiotic pairs which were resistant to isolated organisms. To the best of our knowledge, this is the first study in detecting MDR Enterococcus spp., Salmonella spp., and Vibrio spp. from migratory birds travelling to Bangladesh. Frequent detection of MDR bacteria from migratory birds travelling to Bangladesh suggests that these birds have the potential to carry and spread ABR bacteria and could implicate potential risks to public health. We recommend that these birds should be kept under an AMR surveillance program to minimize the potential risk of contamination of the environment with ABR as well as to reduce their hazardous impacts on health.     

Use of Combined Microautoradiography and Fluorescence In Situ Hybridization To Determine Carbon Metabolism in Mixed Natural Communities of Uncultured Bacteria from the Genus Achromatium

Combined microautoradiography and fluorescence in situ hybridization (FISH) was used to investigate carbon metabolism in uncultured bacteria from the genus Achromatium. All of the Achromatium species identified in a freshwater sediment from Rydal Water, Cumbria, United Kingdom, which were distinguishable only by FISH, assimilated both [¹⁴C]bicarbonate and [¹⁴C]acetate. This extends previous findings that Achromatium spp. present at another location could only utilize organic carbon sources. Achromatium spp., therefore, probably exhibit a range of physiologies, i.e., facultative chemolithoautotrophy, mixotrophy, and chemoorganoheterotrophy, similar to other large sulfur bacteria (e.g., Beggiatoa spp.).     

Taxonomic composition of bacteria associated with cultivated mollusks <Emphasis Type="Italic">Crassostrea lugubris</Emphasis> and <Emphasis Type="Italic">Perna viridis</Emphasis> and with the water of the Gulf of Nha Trang lagoon,Vietnam

One hundred and four strains of heterotrophic bacteria have been isolated and characterized from two species of bivalve mollusks cultivated in the Gulf of Nha Trang (Vietnam) and from the water of a mariculture farm. The isolates have been identified on the basis of morphological, physiological, biochemical, and chemotaxonomic properties, as well as by the content of G+C bases in DNA. In the microflora of mollusks, Vibrio alginolyticus was predominant; the pathogenic species V. harveyi and V. splendidus were found as well. Staphylococci and bacilli occupied the second place in abundance after vibrios. In addition, coryneforms and enterobacteria, as well as Pseudomonas spp. and Pseudoalteromonas spp., were revealed. The composition of the water microflora was more diverse as compared with the microflora of mollusks. In the water, Bacillus spp., Vibrio spp., and Pseudomonas spp. were predominant. Brevibacterium spp. and other coryneform bacteria, as well as enterobacteria, occurred in significant amounts. In addition, Pseudoalteromonas spp., Marinococcus sp., Halobacillus sp., Shewanella sp., Sulfitobacter sp., and bacteria of the CFB cluster were noticed. The presence of pathogenic and conditionally pathogenic bacterial species in the water and mollusks is probably the reason for the high death rate of cultivated animals at the mariculture farm.     

Proteomics‐based identification of orchid-associated bacteria colonizing the Epipactis albensis,E. helleborine and E. purpurata (Orchidaceae,Neottieae)

Using proteomics-based identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), we conducted the first analysis of the composition of endophytic bacteria isolated from different parts of selected Epipactis species, i.e. the buds, the inflorescences and the central part of the shoots, as well as the rhizomes. We identified aerobic and anaerobic bacteria, including such taxa as Bacillus spp., Clostridium spp., Pseudomonas spp. and Stenotrophomonas spp., which may be considered as promoting plant growth. Because most of the indicated bacteria genera belong to spore-producing taxa (spores allow bacterial symbionts to survive adverse conditions), we suggest that these bacteria species contribute to the adaptation of orchids to the environment. We found clear differences in the microbiome between investigated closely related taxa, i.e., Epipactis albensis, E. helleborine, E. purpurata and E. purpurata f. chlorophylla. Some of the analysed orchid species, i.e. E. albensis and E. purpurata co-occur in habitats, and their bacterial microbiomes differ from each other.     

Hormone-Dependent Bacterial Growth,Persistence and Biofilm Formation – A Pilot Study Investigating Human Follicular Fluid Collected during IVF Cycles

Human follicular fluid, considered sterile, is aspirated as part of an in vitro fertilization (IVF) cycle. However, it is easily contaminated by the trans-vaginal collection route and little information exists in its potential to support the growth of microorganisms. The objectives of this study were to determine whether human follicular fluid can support bacterial growth over time, whether the steroid hormones estradiol and progesterone (present at high levels within follicular fluid) contribute to the in vitro growth of bacterial species, and whether species isolated from follicular fluid form biofilms. We found that bacteria in follicular fluid could persist for at least 28 weeks in vitro and that the steroid hormones stimulated the growth of some bacterial species, specifically Lactobacillus spp., Bifidobacterium spp. Streptococcus spp. and E. coli. Several species, Lactobacillus spp., Propionibacterium spp., and Streptococcus spp., formed biofilms when incubated in native follicular fluids in vitro (18/24, 75%). We conclude that bacteria aspirated along with follicular fluid during IVF cycles demonstrate a persistent pattern of growth. This discovery is important since it can offer a new avenue for investigation in infertile couples.     

A survey of outdoor and indoor airborne fungal spora in the Redemption City, Ogun State, south-western Nigeria

The concentration and biodiversity of airborne fungi of the Redemption City, an immense campground for Christian faithful and the temporary site of the Redeemer’s University in south-western Nigeria, was studied between February and May 2011 using the culture plate method. The study was undertaken to assess the concentrations of fungal spores and their health implication in this ever-busy environment. Fifteen different sites classified as closed or open were selected. During the experiment, a total of 228 colonies were counted, and 29 fungal species belonging to 26 genera were isolated which include the following: Aspergillus flavus, Aspergillus niger, Bipolaris spp., Chrysosporium spp., Cladosporium spp., Coniothyrium corda, Curvularia spp., Diplodia spp., Fusarium spp., Gliocladium spp., Monilia spp., Mucor spp., Mucor plumbeus, Penicillium spp., Phycomyces spp., Phytophthora spp., Pilobolus spp., Pyrenochaeta spp., Rhizopus stolonifer, Torula spp., Trichoderma spp. and Trichophyton spp. The most frequently occurring fungi were A. niger, C. corda and M. plumbeus, while the least recorded were Torula and Trichophyton species. Majority of the fungi isolated are known allergens; they could also be opportunistic causing various diseases in man. There is therefore a dire need for good sanitation practices within the studied areas of the camp.     

The bioleaching feasibility for Pb/Zn smelting slag and community characteristics of indigenous moderate-thermophilic bacteria

The feasibility of recovering metal values and removing hazardous elements from the Pb/Zn smelting slag using bioleaching technique were studied through a flask experiment, and the community characteristics of the indigenous moderate-thermophilic bacteria in this bioleaching system were also analyzed through a culture-independent restriction fragment length polymorphism (RFLP) of 16S rRNA genes approach. The results show that more than 80% of Al, As, Cu, Mn, Fe and Zn in the Pb/Zn smelting slag were leached at 65 ^oC, pH 1.5, pulp density 5%, but only about 5% of Pb. Phylogenetic analysis revealed that the bacteria in the bioleaching system mainly fell among Firmicutes, Gammaproteobacteria and Betaproteobacteria, and the dominant bacteria are affiliated with Bacillus spp., Sporosarcina spp. and Pseudomonas spp.     

Improvement of protein bait produced from beer yeast waste for controlling Bactrocera dorsalis (Diptera: Tephritidae) in China

In the present study, preservatives and antibiotics were applied in a variety of doses to assess their effects on the beer waste-based protein bait, a product widely used to control populations of Bactrocera dorsalis (Diptera: Tephritidae). Screening was performed using the inhibition zone method against the dominant bacteria in deteriorated protein bait. Additionally, the attractiveness of the bait was assessed after respectively adding different doses of methyl eugenol, brown sugar solution, ammonium acetate, and guava essence, as determined by bio-cage tests. The results showed that the four selected preservatives had different inhibition effects at different dose levels, and that the level of inhibition increased with dose: at the highest dose of 1:1 (v:v), sodium benzoate can significantly inhibit Staphylococcus spp., potassium sorbate can significantly inhibit Lactobacillus spp., sodium nitrite can significantly inhibit Escherichia spp. and ethyl p-hydroxybenzoate can significantly inhibit Staphylococcus spp. and Xanthomonas spp. Among three antibiotics, kanamycin was the most effective in suppressing a mix of all four bacteria for all tested doses. In terms of lure performance, the addition of four substances in various ratios into the protein bait were found to have varying effects on its attractiveness to B. dorsalis females and males. Specifically, the addition of a high-dose of guava essence could significantly enhance the attractiveness of the bait. Our findings will help to enhance the effectiveness of protein bait applications by prolonging the quality guarantee period and improving its attractiveness toward both female and male B. dorsalis.     

Microbial Ecology of the Gut in Laboratory Stocks of the Migratory Grasshopper, Melanoplus sanguinipes (Fab.) (Orthoptera: Acrididae)

Mean pH values in pooled samples of foregut, midgut, and hindgut from adult Melanoplus sanguinipes, which had been raised in the laboratory on barley shoots and wheat bran, were 5.15, 6.39, and 5.98, respectively. Homogenates of midgut/hindgut sections and frass (feces) yielded colony counts of bacteria by the spread plate method of 5.7 to 5.9 and 5.3 to 5.5 log₁₀ colonies per mg, respectively; there were no significant differences (P > 0.05) between counts obtained on several media or on media incubated aerobically or anaerobically. There was no evidence of significant populations of protozoa, fungi, or obligately anaerobic bacteria associated with the gut. A total of 168 pure strains of bacteria isolated from the gut sections were characterized and assigned to 11 taxonomic groups, including Enterococcus spp., Serratia liquefaciens, Pseudomonas spp., and Enterobacter spp. Numbers of Enterococcus spp. in the gut were 2 to 3 orders of magnitude higher than those of the other genera. Strains representing only four of the groups were recovered from bran fed to the grasshoppers; the barley shoots, which were raised in sterile soil, appeared virtually sterile. Examination of the gut wall by scanning electron microscopy revealed the presence of epimural bacteria in the foregut and hindgut but not in the midgut. The distribution of epimural cocci and bacilli differed with the gut section examined. Numerous spherical to ovoid structures up to 10 μm in diameter, which were not identified, were associated with the microvillous surface of the midgut epithelium. Acetate was present in gut, hemolymph, and frass, and it was shown that representative isolates of Enterococcus spp. and Enterobacter agglomerans produced acetate when incubated in an aqueous suspension of bran. The egestion time of solid digesta, as measured with methylene blue-stained barley shoots, was 3.0 to 5.7 h. The results show that M. sanguinipes supported extensive indigenous populations of luminal and epimural bacteria in the gut which were composed predominantly of facultatively anaerobic species; the relatively short egestion time, indicating rapid passage of digesta through the gut, was consistent with the microscopic appearance of digesta residues in frass and could account, at least in part, for the absence of a significant population of obligately anaerobic bacteria from the gut.     

Distribution and Characterization of Kepone-Resistant Bacteria in the Aquatic Environment

Effects of the chlorinated insecticide Kepone on the ecology of Chesapeake Bay and James River bacteria were studied. Kepone-resistant bacteria present in a given environment were found to reflect the degree of fecal and/or high organic pollution of the sampling sites, based on total numbers and generic composition of the populations of Kepone-resistant bacteria. The presence of Kepone-resistant bacteria was found to be correlated (α = 0.01) with total coliforms, fecal coliforms, and total aerobic viable heterotrophic bacteria, but not with Kepone concentration, since Kepone-resistant bacteria were present in locations where Kepone could not be detected by the analytical methods used in this study. Only gram-negative bacteria, predominantly Pseudomonas, Vibrio, and Aeromonas spp., were found to be resistant to ≥10 μg of Kepone per ml. Gram-positive bacteria, i.e., Bacillus and Corynebacterium spp., were generally sensitive to ≥0.1 μg of Kepone per ml. From results of cluster analysis of taxonomic data, we determined that characteristics of Kepone-resistant bacteria included: resistance to pesticides and heavy metals; degradation of oil; positive oxidase and catalase reactions; and nitrate reduction. From results of the ecological and taxonomic analyses, we conclude that Kepone resistance in estuarine bacteria is due to the physicochemical composition of the gram-negative cell wall and not prior exposure to Kepone. Therefore, the presence of Kepone-resistant bacteria cannot serve as an indicator of Kepone contamination in the aquatic environment where gram-negative bacteria are predominant.     

Distribution, diversity, and activity of sulfate-reducing bacteria in the water column in Gek-Gel lake, Azerbaijan

The distribution and activity of sulfate-reducing bacteria (SRB) in the water column of the alpine meromictic Gek-Gel lake were studied. Apart from traditional microbiological methods based on cultivation and on measuring the process rates with radioactive labels, in situ fluorescent hybridization (FISH) was used, which enables identification and quantification without cultivating organisms. The peak rate of sulfate reduction, 0.486 μg S 1⁻¹ day⁻¹, was found in the chemocline at 33 m. The peak SRB number of 2.5×10⁶ cells/ml, as determined by the most probable number method on selective media, was found at the same depth. The phylogenetic affiliation of the SRB, as determined by FISH, revealed the predominance of the Desulfovibrio spp., Desulfobulbus spp., and Desulfoarculus spp./Desulfomonile spp. groups. The numbers of spore-forming Desulfotomaculum spp. increased with depth. The low measured rates of sulfate reduction accompanied by high SRB numbers and the predominance of the groups capable of reducing a wide range of substrates permit us to assume utilization of electron acceptors other than sulfate as the main activity of the SRB in the water column. Original Russian Text ? O.V. Karnachuk, N.V. Pimenov, S.K. Yusupov, Yu.A. Frank, Ya.A. Puhakka, M.V. Ivanov, 2006, published in Mikrobiologiya, 2006, Vol. 75, No. 1, pp. 101–109.     

Biodiversity of Bacterial Ecosystems in Traditional Egyptian Domiati Cheese

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows: Leuconostoc mesenteroides, Lactococcus garvieae, Aerococcus viridans, Lactobacillus versmoldensis, Pediococcus inopinatus, and Lactococcus lactis. Frequent non-LAB species included numerous coagulase-negative staphylococci, Vibrio spp., Kocuria rhizophila, Kocuria kristinae, Kocuria halotolerans, Arthrobacter spp./Brachybacterium tyrofermentans. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type.     

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus)

The current study provides the insight into the bacteria in the gastrointestinal tract (GIT) and methanogens presented in the rumen and cecum of the Chinese roe deer (Capreolus pygargus). The ruminal, ileal, cecal, and colonic contents, as well as feces, were obtained from each of the three, free-range, roe deer ingesting natural pasture after euthanasia. For the bacterial community, a total of 697,031 high-quality 16S rRNA gene sequences were generated using high-throughput sequencing, and assigned to 2,223 core operational taxonomic units (OTUs) (12 bacterial phyla and 87 genera). The phyla Firmicutes (51.2%) and Bacteroidetes (39.4%) were the dominant bacteria in the GIT of roe deer. However, the bacterial community in the rumen was significantly (P<0.01) different from the other sampled regions along the GIT. Secondly, Prevotella spp., Anaerovibrio spp., and unidentified bacteria within the families Veillonellaceae and Paraprevotellaceae were more abundant in the rumen than in the other regions. Unidentified bacteria within the family Enterobacteriaceae, Succinivibrio spp., and Desulfovibrio spp. were more predominant in the colon than in other regions. Unidentified bacteria within the family Ruminococcaceae, and Bacteroides spp. were more prevalent in the ileum, cecum and fecal pellets. For methanogens in the rumen and cecum, a total of 375,647 high quality 16S rRNA gene sequences were obtained and assigned to 113 core OTUs. Methanobrevibacter millerae was the dominant species accounting for 77.3±7.4 (S.E) % and 68.9±4.4 (S.E) % of total sequences in the rumen and cecum of roe deer, respectively. However, the abundance of Methanobrevibacter smithii was higher in the rumen than in the cecum (P = 0.004). These results revealed that there was intra variation in the bacterial community composition across the GIT of roe deer, and also showed that the methanogen community in the rumen differed from that in the cecum.