Normal conjunctival flora in the North American opossum (Didelphis virginiana) and raccoon (Procyon lotor)

We documented the normal conjunctival bacterial flora from 17 opossums (Didelphis virginiana) and 10 raccoons (Procyon lotor) trapped in Manhattan, Kansas (USA) from November 1999 to January 2000. Both raccoons and opossums were free of apparent ocular disease. The inferior conjunctival sacs of each animal were swabbed for aerobic bacterial and Mycoplasma culture and polymerase chain reaction (PCR) for Mycoplasma and Chlamydia detection. All conjunctival samples were positive for one or more species of aerobic bacteria. The most common isolate from opossums was Staphylococcus spp. Other isolates included Streptococcus spp., Bacillus spp., Corynebacterium spp., and Enterococcus faecalis. The most common isolates in raccoons was Bacillus spp. Other isolates included Streptococcus spp., Staphylococcus spp., non-hemolytic Escherichia coli, and Enterococcus faecalis. Mycoplasma culture was negative in samples from opossums and raccoons. Evidence of Mycoplasma and Chlamydia presence was detected by PCR.     

Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces

Distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (BBD) on the southern Caribbean island of Cura?ao, Netherlands Antilles. PCR amplification and sequencing of bacterial 16S rRNA genes (rDNA) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. The molecular sequences exhibited less than 5% similarity in bacterial community composition between seawater and the healthy, black band diseased, and dead coral surfaces. The BBD bacterial mat rapidly migrates across and kills the coral tissue. Clone libraries constructed from the BBD mat were comprised of eight bacterial divisions and 13% unknowns. Several sequences representing bacteria previously found in other marine and terrestrial organisms (including humans) were isolated from the infected coral surfaces, including Clostridium spp., Arcobacter spp., Campylobacter spp., Cytophaga fermentans, Cytophaga columnaris, and Trichodesmium tenue.     

Phylogenetic analysis of a biofilm bacterial population in a water pipeline in the Gulf of Mexico

The aim of this study was to assess the bacterial diversity associated with a corrosive biofilm in a steel pipeline from the Gulf of Mexico used to inject marine water into the oil reservoir. Several aerobic and heterotrophic bacteria were isolated and identified by 16S rRNA gene sequence analysis. Metagenomic DNA was also extracted to perform a denaturing gradient gel electrophoresis analysis of ribosomal genes and to construct a 16S rRNA gene metagenomic library. Denaturing gradient gel electrophoresis profiles and ribosomal libraries exhibited a limited bacterial diversity. Most of the species detected in the ribosomal library or isolated from the pipeline were assigned to Proteobacteria (Halomonas spp., Idiomarina spp., Marinobacter aquaeolei, Thalassospira sp., Silicibacter sp. and Chromohalobacter sp.) and Bacilli (Bacillus spp. and Exiguobacterium spp.). This is the first report that associates some of these bacteria with a corrosive biofilm. It is relevant that no sulfate-reducing bacteria were isolated or detected by a PCR-based method. The diversity and relative abundance of bacteria from water pipeline biofilms may contribute to an understanding of the complexity and mechanisms of metal corrosion during marine water injection in oil secondary recovery.     

Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches

Bacterial communities in both aqueous and oil phases of water-flooded petroleum reservoirs were characterized by molecular analysis of bacterial 16S rRNA genes obtained from Shengli Oil Field using DNA pyrosequencing and gene clone library approaches. Metagenomic DNA was extracted from the aqueous and oil phases and subjected to polymerase chain reaction amplification with primers targeting the bacterial 16S rRNA genes. The analysis by these two methods showed that there was a large difference in bacterial diversity between the aqueous and oil phases of the reservoir fluids, especially in the reservoirs with lower water cut. At a high phylogenetic level, the predominant bacteria detected by these two approaches were identical. However, pyrosequencing allowed the detection of more rare bacterial species than the clone library method. Statistical analysis showed that the diversity of the bacterial community of the aqueous phase was lower than that of the oil phase. Phylogenetic analysis indicated that the vast majority of sequences detected in the water phase were from members of the genus Arcobacter within the Epsilonproteobacteria, which is capable of degrading the intermediates of hydrocarbon degradation such as acetate. The oil phase of reservoir fluid samples was dominated by members of the genus Pseudomonas within the Gammaproteobacteria and the genus Sphingomonas within the Alphaproteobacteria, which have the ability to degrade crude oil through adherence to hydrocarbons under aerobic conditions. In addition, many anaerobes that could degrade the component of crude oil were also found in the oil phase of reservoir fluids, mainly in the reservoir with lower water cut. These were represented by Desulfovibrio spp., Thermodesulfovibrio spp., Thermodesulforhabdus spp., Thermotoga spp., and Thermoanaerobacterium spp. This research suggested that simultaneous analysis of DNA extracted from both aqueous and oil phases can facilitate a better understanding of the bacterial communities in water-flooded petroleum reservoirs.     

Taxonomic composition of bacteria associated with cultivated mollusks Crassostrea lugubris and Perna viridis 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.     

Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens

The gastrointestinal tract is a dynamic ecosystem containing a complex microbial community. In this paper, the indigenous intestinal bacteria and the microbial fermentation profile particularly short chain fatty acids (SCFA), lactate, and ammonia concentrations are reviewed. The intestinal bacterial composition changes with age. The bacterial density of the small intestine increases with age and comprises of lactobacilli, streptococci, enterobacteria, fusobacteria and eubacteria. Strict anaerobes (anaerobic gram-positive cocci, Eubacterium spp., Clostridium spp., Lactobacillus spp., Fusobacterium spp. and Bacteroides) are predominating caecal bacteria in young broilers. Data from culture-based studies showed that bifidobacteria could not be isolated from young birds, but were recovered from four-week-old broilers. Caecal lactobacilli accounted for 1.5-24% of the caecal bacteria. Gene sequencing of caecal DNA extracts showed that the majority of bacteria belonged to Clostridiaceae. Intestinal bacterial community is influenced by the dietary ingredients, nutrient levels and physical structure of feed. SCFA and other metabolic products are affected by diet formulation and age. Additional studies are required to know the bacterial metabolic activities together with the community analysis of the intestinal bacteria. Feed composition and processing have great potential to influence the activities of intestinal bacteria towards a desired direction in order to support animal health, well-being and microbial safety of broiler meat.     

Partitioning of Bacterial Communities between Seawater and Healthy, Black Band Diseased, and Dead Coral Surfaces

Distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (BBD) on the southern Caribbean island of Curaçao, Netherlands Antilles. PCR amplification and sequencing of bacterial 16S rRNA genes (rDNA) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. The molecular sequences exhibited less than 5% similarity in bacterial community composition between seawater and the healthy, black band diseased, and dead coral surfaces. The BBD bacterial mat rapidly migrates across and kills the coral tissue. Clone libraries constructed from the BBD mat were comprised of eight bacterial divisions and 13% unknowns. Several sequences representing bacteria previously found in other marine and terrestrial organisms (including humans) were isolated from the infected coral surfaces, including Clostridium spp., Arcobacter spp., Campylobacter spp., Cytophaga fermentans, Cytophaga columnaris, and Trichodesmium tenue.     

Treatment of sanitary-important bacteria by bacteriocin substance V24 in cattle dung water

Quantification of sanitary-important bacteria (e.g. Enterobacteriaceae), as well as indicators of environmental contamination, was assessed in samples of cattle dung from 25 cattle farms in 15 north-eastern Slovakia districts. The inhibitory effect of crude bacteriocin extract CBE V24 from Enterococcus faecalis V24 against Listeria monocytogenes Ohio and Yersinia enterocolitica YE85 was examined in cattle dung water with the aim of finding a new way of eliminating the health risk of the animal slurry. The following bacterial groups were quantified: Salmonella spp., Shigella-like spp. , Proteus spp., Enterobacter spp., Citrobacter spp., Pseudomonas spp. , Escherichia coli, Listeria spp., staphylococci, streptococci and enterococci (the average count ranged from 102 up to 104 cfu ml-1). Antagonistic effect of the crude bacteriocin from Enterococcus faecalis V24 in the range of 100-600 Arbitrary units per ml (AU ml-1) was shown against the following bacteria: Enterobacter cloacae, Ent. asburiae, Proteus spp., Salmonella spp., Acinetobacter lwoffi, L. monocytogenes as well as Y. enterocolitica YE85. During tests performed to study the inhibitory effect of the crude bacteriocin CBE V24 (concentration 800, 1600 AU ml-1) against L. monocytogenes Ohio and Y. enterocolitica YE85 in experimentally contaminated cattle dung, a reduction of 2.03 and 1.44 log cfu ml-1, respectively, was already noted after 1 h after crude bacteriocin CBE V24 addition.     

Influence of substances produced by lipophilic Corynebacterium CDC G1 ZMF 3P13 on the microorganisms inhabiting human skin

Lipophilic species of Corynebacterium inhabiting skin as residents produces substances that can regulate the composition of natural flora. Research that was carried out concerned an influence of the substances produced by Corynebacterium CDC G1 ZMF 3P13 on the set of 22 bacterial strains (Staphylococcus spp., Corynebacterium spp., Propionibacterium spp.) mutually existing on the skin and the set of 6 Candida spp. isolated from patients. It was found out that the strain gives off into environment a mixture of substances with opposite effects. In the course of research an inhibiting substance (BLIS) was isolated with its evident effect on S. aureus, S. epidermidis, C. diphtheriae i Propionibacterium spp.     

Tick-borne infections as a cause of heart transplantation

Many bacterial species can be a cause of various heart diseases, such as: Borrelia burgdorferi sensu lato, Coxiella burnetii and Bartonella spp. The aim of the present studies was to establish if any tick-borne infections can contribute to serious heart disorders resulting in the need for heart transplantation. Myocardium, aortic and mitral valve samples from hearts removed from patients undergoing heart transplantation were tested. The presence of Bartonella spp., Borrelia afzeli and C. burnetii bacteria in malfunctioning human hearts has been shown. DNA of Bartonella spp., B. burgdorferi and C. burnetii were detected in various parts of tested hearts. DNA of B. afzelii and Bartonella spp. were found in the aortic valves. DNA of C. burnetii was detected in the myocardium. Mixed infections with Bartonella spp. and C. burnetii were also observed. Obtained results indicate that diagnosis of Bartonella spp., B. burgdorferi C. burnetii and Rickettsia spp. infections should be considered in cases of infectious endocarditis with negative blood cultures.     

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.     

Phylogenetic characterization of the heterotrophic bacterial communities inhabiting a marine recirculating aquaculture system

Aims: The aim of the present work was to characterize the heterotrophic bacterial community of a marine recirculating aquaculture system (RAS). Methods and Results: An experimental RAS was sampled for the rearing water (RW) and inside the biofilter. Samples were analysed for bacterial abundances, community structure and composition by using a combination of culture‐dependent and ‐independent techniques. The most represented species detected among biofilter clones was Pseudomonas stutzeri, while Ruegeria spp. and Roseobacter spp. were more abundant among isolates. In comparison, the genera Roseobacter and Ruegeria were well represented in both the biofilter and the RW samples. A variety of possible bacterial pathogens (e.g. Vibrio spp., Erwinia spp. and Coxiella spp.) were also identified in this study. Conclusions: Results revealed that the bacterial community in the RW was quite different to that associated with the biofilter. Moreover, data obtained suggest that the whole bacterial community can be involved in maintaining an effective and a stable rearing environment (shelter effect). Significance and Impact of the Study: Improving the reliability and the sustainability of RAS depends on the correct management of the bacterial populations inside it. This study furnishes more accurate information on the bacterial populations and better clarifies the existing relationships between the bacterial flora in the RW and that associated with the biofilter.     

Bacterial flora from bronchoalveolar lavage and occurrence of class IgG and IgA antibodies to Chlamydia pneumoniae in patients with chronic obstructive pulmonary disease (COPD)

Bronchoalveolar lavage taken from 46 patients (ranging in age from 21 to 71 years, mean 50.6 +/- 13.9) was examined for aerobic and anaerobic bacterial flora. Sera taken from 39 of patients as well as sera taken from 25 healthy blood donors of similar age (P = 0.99) were examined to determine IgG and IgA antibodies to C. pneumoniae. Bacterial flora was routinely cultured and determined using ATB computer system (bioMérieux,). IgG and IgA antibodies were tested by the enzyme immunoassays (Labsystems, Finland, Helsinki). Sera containing anti -C. pneumoniae IgG antibodies with titers of 45 EIU or higher and IgA with titers of 12 EIU or higher were considered positive. 143 of aerobic and 74 of anaerobic bacterial strains were cultured. Streptococci group viridans, pneumococci, enteric bacilli, Haemophilus spp., Prevotella spp., Actinomyces spp., Bifidobacterium spp. and Veilonella spp. were most often cultured. 66.6% of patients had IgG or IgA antibodies, in contrast, to the control group in which 60.0% and 44.0% of examined blood donors had IgG and IgA antibodies respectively. COPD patients were more frequently positive for specific anti-C. pneumoniae antibodies than the healthy donors (p = 0.003). The difference in a seropositivity rate of specific IgA and IgG antibodies was significant (p = 0.00002 and p = 0.003 respectively). Bronchoalveolar lavage of patients suffering from COPD can be contaminated with high number of aerobic and anaerobic bacterial species, and immunological status of the patients indicated persistent infection caused by C. pneumoniae more often than in controls.     

Intestinal carriage of campylobacters, salmonellas, yersinias and listerias in pigeons in the city of Barcelona

L. CASANOVAS, M. DE SIMÓN, M.D. FERRER, J. ARQUÉS AND G. MONZÓN. 1995. The faecal bacterial flora of pigeons, which may be the source of infectious diseases in man, was studied in the city of Barcelona. Four hundred cloacal specimens were examined for Campylobacter jejuni, Camp. coli, Salmonella spp., Yersinia spp. and Listeria spp., over a 12 month period.
Campylobacter jejuni was the most frequently isolated micro-organism, found in 105 pigeons (26.2%), with a greater incidence in the districts of the city with a high density of pigeons and without seasonal variation. Salmonella spp. were isolated from six specimens (1.5%) and Yersinia intermedia was isolated from only one pigeon.     

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.     

Allogenic succession of marine bacterial communities in response to pharmaceutical waste

Vibrio spp. predominated in the culturable bacterial community of surface waters of the Puerto Rico Trench at the site of disposal for nearly ten years of pharmaceutical wastes. In this area and surrounding waters as far as 1000 km north of the dumpsite and south into the Caribbean Sea, Vibrio spp. comprised up to 100% of the culturable bacteria, with Acinetobacter spp. being the second most prevalent group. Pseudomonas spp., reported to be common in these waters a decade earlier, were virtually absent from all samples examined during a three year study involving 9 cruises. Staphylococcus spp. were also found in water samples collected within the dumpsite. Using cultures isolated from surface water samples collected at the dumpsite, laboratory experiments confirmed that pharmaceutical waste can enrich for Vibrio spp., in preference to Pseudomonas spp., with growth of the strains proportional to the amount of waste added.     

Allogenic succession of marine bacterial communities in response to pharmaceutical waste

Vibrio spp. predominated in the culturable bacterial community of surface waters of the Puerto Rico Trench at the site of disposal for nearly ten years of pharmaceutical wastes. In this area and surrounding waters as far as 1000 km north of the dumpsite and south into the Caribbean Sea, Vibrio spp. comprised up to 100% of the culturable bacteria, with Acinetobacter spp. being the second most prevalent group. Pseudomonas spp., reported to be common in these waters a decade earlier, were virtually absent from all samples examined during a three year study involving 9 cruises. Staphylococcus spp. were also found in water samples collected within the dumpsite. Using cultures isolated from surface water samples collected at the dumpsite, laboratory experiments confirmed that pharmaceutical waste can enrich for Vibrio spp., in preference to Pseudomonas spp., with growth of the strains proportional to the amount of waste added.     

七味白术散对菌群失调腹泻小鼠肠道细菌多样性的影响

【背景】肠道微生物与人体多项生理功能密切相关,我们课题组前期研究表明七味白术散对菌群失调腹泻有较好的疗效。【目的】探讨与七味白术散疗效相关肠道微生物,比较传统中药饮片与超微中药饮片的疗效,进一步明确七味白术散治疗菌群失调腹泻的机理,为临床应用提供科学依据。【方法】应用抗生素建立菌群失调小鼠腹泻模型,分别灌胃给药七味白术散传统汤剂和超微50%量七味白术散汤剂。治疗结束后,提取肠道内容物微生物宏基因组DNA,建立16S rRNA基因文库进行测序。【结果】肠道微生物中的群落由乳酸菌(Lactobacillus spp.)、屎肠球菌(Enterococcus feacium)、梭状芽孢杆菌(Clostridium spp.)、黏液真杆菌(Blautia producta)、毛螺旋菌(Anaerostipes spp.)、腐生性葡萄球菌(Staphylococcus saprophyticus)和不能培养的细菌组成,其中乳酸菌为优势菌,占全部细菌DNA克隆数的61.90%。经抗生素造模后Lactobacillus spp.数量明显减少,Enterococcus feacium成为优势菌种,Clostridium spp.、Blautia product、Anaerostipes spp.和Staphylococcus saprophyticus等在数量上开始有增长的趋势,而治疗结束后,传统七味白术散治疗组和超微50%量七味白术散治疗组的Lactobacillus spp.比例均有所恢复,且超微50%量七味白术散治疗组的乳酸菌比例与正常组最接近;通过建立聚类树和计算各组中各菌群的多样性(H)、丰富度(S)、均匀度(E)及优势度指数(D)可知,超微50%量七味白术散治疗组可与正常组聚为一类,且超微50%量七味白术散治疗组各项指数与正常组最为接近,说明超微50%量七味白术散治疗组肠道微生物的基因文库及多样性与正常组最接近,超微50%量七味白术散汤剂的治疗效果优于七味白术散传统汤剂。【结论】应用16S rRNA基因克隆文库技术进一步明确了正常小鼠肠道中细菌群落的组成,以及七味白术散对菌群失调腹泻小鼠肠道细菌群落的恢复效果,超微50%量七味白术散汤剂的治疗效果优于七味白术散传统汤剂。     

Acidified litter benefits the intestinal flora balance of broiler chickens

The alterations in the balance of the normal intestinal bacterial flora of chickens exposed to acidified wood-derived litter were analyzed and compared to those of a control group exposed to nonacidified litter. A total of 1,728 broilers were divided into two groups, with six replicates in each. One group was exposed to dry wood-derived litter, and the other was exposed to dry wood-derived litter sprayed with a mixture of sodium lignosulfonate, formic acid, and propionic acid. At five different times, five chickens from each pen were killed and the intestinal contents from ileum and caeca were collected. The samples were diluted and plated onto selective media to identify coliforms, Lactobacillus spp., Clostridium perfringens, and Enterococcus spp. Covariance analysis of bacterial counts showed significantly lower counts for C. perfringens in the caeca and the ileum and for Enterococcus spp. and Lactobacillus spp. in the ileum in chickens exposed to the acidified litter. Lactobacillus spp. showed significantly higher counts in the caeca in chickens exposed to acidified litter. There was no difference between the two litters with regard to coliforms in the ileum and the caeca or to Enterococcus spp. in the caeca. The study shows that exposing the chickens to acidified litter lowers the intestinal bacterial number, especially in the ileum, without negative consequences for the chicken's health or performance. Of special interest are the lower counts of C. perfringens and Enterococcus spp. that might reduce the risk of developing clinical or subclinical necrotic enteritis and growth depression.     

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.