The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters

Cellulose is reputedly the most abundant organic polymer in the biosphere, yet despite the fundamental role of cellulolytic microorganisms in global carbon cycling and as potential sources of novel enzymes for biotechnology, their identity and ecology is not well established. Cellulose is a major component of landfill waste and its degradation is therefore a key feature of the anaerobic microbial decomposition process. Here, we targeted a number of taxa containing known cellulolytic anaerobes (members of the bacterial genus Fibrobacter, lineages of Clostridium clusters I, III, IV and XIV, and anaerobic fungi of the Neocallimastigales) in landfill leachate and colonized cellulose 'baits' via PCR and quantitative PCR (qPCR). Fibrobacter spp. and Clostridium clusters III, IV and XIV were detected in almost all leachate samples and cluster III and XIV clostridia were the most abundant (1-6% and 1-17% of total bacterial 16S rRNA gene copies respectively). Two landfill leachate microcosms were constructed to specifically assess those microbial communities that colonize and degrade cellulose substrates in situ. Scanning electron microscopy (SEM) of colonized cotton revealed extensive cellulose degradation in one microcosm, and Fibrobacter spp. and Clostridium cluster III represented 29% and 17%, respectively, of total bacterial 16S rRNA gene copies in the biofilm. Visible cellulose degradation was not observed in the second microcosm, and this correlated with negligible relative abundances of Clostridium cluster III and Fibrobacter spp. (≤ 0.1%), providing the first evidence that the novel fibrobacters recently detected in landfill sites and other non-gut environments colonize and degrade cellulose substrates in situ.     

Quantitative method for measurement of aerotolerance of bacteria and its application to oral indigenous anaerobes

An index which expressed the aerobic to anaerobic potential was made for bacteria with intermediate tolerance for oxygen. One method used for this analysis was measurement of the relative bacterial growth ratio. The other method was based on the pattern of the absorbancy versus depth plot. The index was applied to oral indigenous anaerobes.     

Quantitative method for measurement of aerotolerance of bacteria and its application to oral indigenous anaerobes.

An index which expressed the aerobic to anaerobic potential was made for bacteria with intermediate tolerance for oxygen. One method used for this analysis was measurement of the relative bacterial growth ratio. The other method was based on the pattern of the absorbancy versus depth plot. The index was applied to oral indigenous anaerobes.     

Oral Colonization of Fungi

Opportunistic microbes are able to exist as commensals or pathogens depending on local environmental conditions. The bacterial microbiome at mucosal sites (gut, oral and vaginal) has been well characterized but there has been less focus on the fungal component of the microbiome, the “mycobiome”, especially of the oral mucosa. Genomic characterization studies have shown that Candida species are the most prevalent fungal species in the mycobiomes of the murine gut and human oral cavity, with C. albicans being the most abundant fungal species in the oral cavity. In this review, we outline recent advances in the characterization of the oral mycobiome, how different Candida species colonize, invade and infect the oral cavity, and how epithelial surfaces play a key role in antifungal activity and discriminate between commensal and pathogenic Candida.     

Biphasic assembly of the murine intestinal microbiota during early development

The birth canal provides mammals with a primary maternal inoculum, which develops into distinctive body site-specific microbial communities post-natally. We characterized the distal gut microbiota from birth to weaning in mice. One-day-old mice had colonic microbiota that resembled maternal vaginal communities, but at days 3 and 9 of age there was a substantial loss of intestinal bacterial diversity and dominance of Lactobacillus. By weaning (21 days), diverse intestinal bacteria had established, including strict anaerobes. Our results are consistent with vertical transmission of maternal microbiota and demonstrate a nonlinear ecological succession involving an early drop in bacterial diversity and shift in dominance from Streptococcus to Lactobacillus, followed by an increase in diversity of anaerobes, after the introduction of solid food. Mammalian newborns are born highly susceptible to colonization, and lactation may control microbiome assembly during early development.     

Anaerobes in the Nasopharynx During Acute Otitis Media Episodes in Infancy

The present study, as a part of our longitudinal study on the development of the nasopharyngeal microflora, investigates the nasopharyngeal carriage of anaerobes during 75 episodes of acute otitis media (AOM) experienced by 34 infants during their first 2 years of life. Special emphasis was put on adequate methods of detecting anaerobic bacteria from carefully collected nasopharyngeal aspirates. During the follow-up period, two-thirds of the infants carried anaerobes in the nasopharynx at least once. Anaerobic species were recovered from 47% of the nasopharyngeal aspirates. Environmental/ecological changes in the nasopharynx during infection favour the growth of anaerobes. Their significance in the pathogenesis of AOM, if any, warrants further study.     

Bacterial colonization of minerals in grassland soils is selective and highly dynamic

Bacteria colonize reactive minerals in soils where they contribute to mineral weathering and transformation. So far, the specificity, patterns and dynamics of mineral colonization have rarely been assessed under natural conditions. High throughput Illumina sequencing was employed to investigate the bacterial communities assembling on illite and goethite during exposure to natural grassland soils. Two different types of organic carbon sources, simple carbon compounds representing root exudates and detritus of two dominant grassland plant species were applied, and their effects on the temporal dynamics of bacterial communities were investigated. The observed temporal patterns suggest that the surfaces of de novo exposed minerals in soils drive the establishment of bacterial communities and override the effect of the type of carbon sources and of other environmental properties. Mineral colonization was selective and specific bacterial sequence variants exhibited distinct colonization patterns, among which early, intermittent, and late colonizers could be distinguished. Based on our results, soil minerals are not only colonized by specific bacterial communities but enable a succession of different bacterial communities. Our results thereby expand the concept of the mineralosphere and provide novel insights into mechanisms of community assembly in the soil ecosystem.     

The Microbiome of the Middle Meatus in Healthy Adults

Rhinitis and rhinosinusitis are multifactorial disease processes in which bacteria may play a role either in infection or stimulation of the inflammatory process. Rhinosinusitis has been historically studied with culture-based techniques, which have implicated several common pathogens in disease states. More recently, the NIH Human Microbiome Project has examined the microbiome at a number of accessible body sites, and demonstrated differences among healthy and diseased patients. Recent DNA-based sinus studies have suggested that healthy sinuses are not sterile, as was previously believed, but the normal sinonasal microbiome has yet to be thoroughly examined. Middle meatus swab specimens were collected from 28 consecutive patients presenting with no signs or symptoms of rhinosinusitis. Bacterial colonization was assessed in these specimens using quantitative PCR and 16S rRNA pyrosequencing. All subjects were positive for bacterial colonization of the middle meatus. Staphylococcus aureus, Staphylococcus epidermidis and Propionibacterium acnes were the most prevalent and abundant microorganisms detected. Rich and diverse bacterial assemblages are present in the sinonasal cavity in the normal state, including opportunistic pathogens typically found in the nasopharynx. This work helps establish a baseline for understanding how the sinonasal microbiome may impact diseases of the upper airways.     

Anaerobic bacteria in clinical infections

The findings of 275 cultures from routine clinical specimens obtained from lesions in different sites of body, during a period of 11 months, are presented. The clinical specimens were obtained from surgical wounds, abdominal infections, orthopaedic operations, biliary tract infections and pleuropulmonary infections. The total number of positive cultures including both aerobes and anaerobes was 203 out of 275 (73.8%). Of the 38 cultures positive for anaerobes, 29 (76.3%) grew both aerobic and anaerobic bacteria, while in nine (23.7%) cultures only anaerobes were found. A total of 42 strains of anaerobic bacteria were isolated. The majority of them were found in clinical specimens obtained from abdominal infections (62%), while a low percentage (3.6%) was found in specimens from orthopaedic operations. Strains belonging to the genus Bacteroides were the most frequently isolated anaerobes, accounting for 35.7% of the total, followed by Clostridia 28.5%, Peptostreptococci 23.8% and Prevotella 12%.     

Diversity and dynamics of bacteriocins from human microbiome

Human commensal microbiota are an important determinant of health and disease of the host. Different human body sites harbour different bacterial microbiota, bacterial communities that maintain a stable balance. However, many of the factors influencing the stabilities of bacterial communities associated with humans remain unknown. In this study, we identified putative bacteriocins produced by human commensal microbiota. Bacteriocins are peptides or proteins with antimicrobial activity that contribute to the stability and dynamics of microbial communities. We employed bioinformatic analyses to identify putative bacteriocin sequences in metagenomic sequences obtained from different human body sites. Prevailing bacterial taxa of the putative bacteriocins producers matched the most abundant organisms in each human body site. Remarkably, we found that samples from different body sites contain different density of putative bacteriocin genes, with the highest in samples from the vagina, the airway, and the oral cavity and the lowest in those from gut. Inherent differences of different body sites thus influence the density and types of bacteriocins produced by commensal bacteria. Our results suggest that bacteriocins play important roles to allow different bacteria to occupy several human body sites, and to establish a long‐term commensal relationship with human hosts.     

The genus Prevotella in cystic fibrosis airways

Airway disease resulting from chronic bacterial colonization and consequential inflammation is the leading cause of morbidity and mortality in patients with Cystic Fibrosis (CF). Although traditionally considered to be due to only a few pathogens, recent re-examination of CF airway microbiology has revealed that polymicrobial communities that include many obligate anaerobes colonize lower airways. The purpose of this study was to examine Prevotella species in CF airways by quantitative culture and phenotypic characterization. Expectorated sputum was transferred to an anaerobic environment immediately following collection and examined by quantitative microbiology using a variety of culture media. Isolates were identified as facultative or obligate anaerobes and the later group was identified by 16S rRNA sequencing. Prevotella spp. represented the majority of isolates. Twelve different species of Prevotella were recovered from 16 patients with three species representing 65% of isolates. Multiple Prevotella species were often isolated from the same sputum sample. These isolates were biochemically characterized using Rapid ID 32A kits (BioMérieux), and for their ability to produce autoinducer-2 and β-lactamases. Considerable phenotypic variability between isolates of the same species was observed. The quantity and composition of Prevotella species within a patients’ airway microbiome varied over time. Our results suggest that the diversity and dynamics of Prevotella in CF airways may contribute to airway disease.     

Bacterial colonization of the oral cavity of the BALB/c mouse

The acquisition of the human oral bacterial flora follows a relatively well known sequence of succession that can be influenced by various host factors. These factors have not been studied in the mouse. In the present work, we followed the bacterial colonization of the oral cavity of mice from birth, and tested our mouse model for its suitability in studying the influence of weaning and puberty on the indigenous oral bacterial flora. We observed that the first colonizers were staphylococci, followed by lactobacilli. The proportions of these two predominant bacteria fluctuated for a period of 30–50 days, but evolved towards the proportions previously observed among the indigenous bacterial species of 6–8 week-old BALB/c male mice (predominantly Lactobacillus murinus and Staphylococcus aureus). The weaning period significantly altered the equilibrium among the oral bacterial flora. This equilibrium was not significantly modified during puberty. Offprint requests to: M.C. Lavoie     

Nestedness of hoopoes' bacterial communities: symbionts from the uropygial gland to the eggshell

How microbial symbionts are established and maintain on their hosts is a leading question with important consequences for the understanding of the evolution and functioning of mutualistic relationships. The acquisition by hosts of mutualistic microbial symbionts can be considered as colonization processes of environments (i.e., host) by symbionts. Colonization processes can be explored by characterizing the nestedness of communities, but this approach has rarely been applied to communities of microbial symbionts. We used this approach here, and estimated the nestedness of bacterial communities of hoopoes (Upupa epops), a species with symbiotic bacteria in their uropygial gland that are expected to colonize eggshells where they protect embryos from pathogens. Bacterial communities were characterized by ARISA (Automated rRNA Intergenetic Spacer Region) and studied the nestedness characteristics of bacterial communities living in the uropygial secretion, bill, belly and eggshells of each sampled female hoopoes. We detected a consistent nested pattern of bacterial communities of hoopoes; from the uropygial gland to the eggshell. We also found evidence of study year and reproductive events influencing the level of nestedness of bacterial communities of hoopoes. These results indicate that bacterial communities of eggshells and body parts of female hoopoes are at least partially conditioned by the symbiotic community in the uropygial gland. We discuss the importance of these results for understanding this host–microbial mutualism functioning and evolution.     

Pathogenic synergy: mixed infections in the oral cavity

In almost all infections in the oral cavity, mixed populations of bacteria are present. However, recent evidence points to a certain specificity in these infections:Streptococcus mutans is related to caries and black-pigmentedBacteroides species are suspected pathogens in periodontal disease. Periodontal diseases, endodontic infections and submucous abscesses in the oral cavity are probably mixed infections in which anaerobic bacteria together with facultatives or other anaerobes are present. In experimental mixed anaerobic infections black-pigmentedBacteroides strains have been shown to play a key role. Little is known about the pathogenic synergy between the bacteria involved in mixed infections. Important mechanisms could be nutritional interrelationships and interactions with the host defense. Within the group of black-pigmentedBacteroides B. gingivalis seems to be the most virulent species. These bacteria possess a great number of virulence factors, which might be important in the pathogenesis of oral infections.     

Anaerobic infections in children

Anaerobic bacteria can cause a variety of endogenous infections in children. Because of their fastidious nature, they are difficult to isolate from infectious sites, and are often overlooked. Anaerobic infections can occur in all body sites, including the central nervous system, oral cavity, head and neck, chest, abdomen, pelvis, skin, and soft tissues. They colonize the newborn after delivery and have been recovered from several types of neonatal infections. These include cellulitis of the site of fetal monitoring, neonatal aspiration pneumonia, bacteremia, conjunctivitis, omphalitis, and infant botulism. The lack of adequate therapy may lead to clinical failures. Their isolation requires appropriate methods of collection, transportation and cultivation of specimens. Treatment is complicated by their slow growth, their polymicrobial nature and their growing resistance to antimicrobials. Antimicrobial therapy is often the only form of therapy required, whereas in others it is an important adjunct to a surgical approach. Because anaerobes are generally recovered mixed with aerobic organisms, the choice of antimicrobial agents should provide coverage of both types of pathogens.     

T cell knockout mice have diminished alveolar bone loss after oral infection with Porphyromonas gingivalis

Periodontal diseases are chronic inflammatory diseases that can result in resorption of the alveolar bone of the jaw. We have developed a murine model in which alveolar bone loss is induced by oral infection with Porphyromonas gingivalis, an oral anaerobic bacterium associated with periodontal disease in humans. Here we compared a strain of immunocompetent mice (C57BL/6J) to the same strain of mice made T cell deficient by genetic deletion of the alpha chain of their T cell receptors (C57BL/6J-Tcra). T cell deficiency did not affect the ability of P. gingivalis to implant in the oral cavity. The two strains of mice had equal percentages of P. gingivalis among their cultivable anaerobes 7 weeks after infection. The same bacterial load led to much less bone resorption in the T cell deficient mice than in the immune normal mice, measured as either the number of sites with significant loss, or as the total amount of bone resorbed. T cell deficient mice lost bone at only three out of 14 measurement sites, compared with eight out of 14 sites in the wild-type mice. The total amount of bone lost was 70% less in the T cell deficient mice. T cell deficient mice had lower titers of P. gingivalis-specific IgG than the wild-type mice after oral infection did, but the same titers of specific IgA. Lower titers did not correlate with greater bone loss. Antigen-activated T lymphocytes are known to induce osteoclastogenesis; here we demonstrate that T cell deletion decreases the amount of alveolar bone loss induced by infection of the murine oral cavity.     

Colonization and turnover of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in otitis-prone children

Recurrent otitis media are frequently intractable during childhood. It is unclear whether recurrent otitis media is caused by etiological bacteria colonization or by new infections. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis were isolated from the nasopharynx of 7 otitisprone and 2 non-prone children with recurrent otitis media. Plural bacterial species and strains were found in all children while affected by otitis media. The same strain was repeatedly isolated from all otitisprone children even after administration of antibiotics but was not from the non-prone children. Antibiotic susceptibility did not differ significantly among the same repeatedly isolated strains. This pilot study suggests that the etiological bacteria tend to colonize and is hard to eliminate in otitis-prone children.     

应用遗传改造的沙门菌介导肿瘤治疗的研究进展

肿瘤是机体在各种致瘤因子作用下,局部组织细胞异常增生所形成的赘生物。肿瘤治疗一直是临床上的一个难题,而放疗、化疗和手术等常规的肿瘤治疗方法均具有明显的局限性。早期研究发现某些厌氧菌或兼性厌氧菌具有抗肿瘤效应,例如兼性厌氧菌鼠伤寒沙门氏菌可以通过某些机制选择性定殖于肿瘤并抑制肿瘤生长,其应用于肿瘤治疗具有许多潜在的优势。过去的一二十年里,已有不少研究者通过遗传操作减弱沙门菌毒力,提高其定殖肿瘤的靶向性,或以减毒沙门菌作为载体向肿瘤靶向递呈各种治疗分子,并在许多动物试验中观察到遗传改造沙门菌的良好抗肿瘤效应。随着沙门菌抗肿瘤研究的不断深入,应用遗传改造的沙门菌有希望成为一条更有效的肿瘤治疗途径。本文将从沙门菌的抗肿瘤机制、遗传改造的沙门菌介导肿瘤治疗的研究进展和目前研究存在的问题等方面进行综述。     

Identification and characterization of a cell envelope protein of Haemophilus influenzae contributing to phase variation in colony opacity and nasopharyngeal colonization

Haemophilus influenzae undergoes spontaneous phase variation in colony morphology. Organisms from transparent colonies efficiently colonize the nasopharynx in an infant rat model of H. influenzae carriage, whereas organisms from more opaque colonies are deficient at colonization. A genetic approach relying on the transformability of H. influenzae was used to identify a locus contributing to opacity variation. By screening a library of chomosomal DNA from an opaque variant of strain Rd, it was possible to isolate a single clone capable of transforming a transparent Rd host to a more opaque phenotype. A region containing two genes, designated oapA and oapB , was identified. The deduced amino acid sequence of oapB has similarity to a consensus sequence for bacterial lipoproteins. Genetically defined mutations in oapA were transformed into the transparent Rd to confirm that this gene is required for expression of the transparent colony phenotype. Although oapA lacks a signal sequence, gene fusions to phoA show that OapA is secreted in H. influenzae and undergoes phase variation in expression. Mutagenesis of oapA in strain Rd, and type b strain Eagan, resulted in loss of the ability to colonize the nasopharynx of infant rats. The type b mutant, however, was as virulent as its parent strain when inoculated intraperitoneally. This suggests that the contribution of OapA to pathogenesis is limited to events associated with colonization of the mucosal surface.     

pH and Eh in Single and Mixed Culture Bacterial Plaque in an Artificial Mouth

The pH and E h of bacterial plaques produced on a tooth surface in an artificial mouth following inoculation with saliva, single cultures and mixed cultures were measured. The importance of these properties and the role of sucrose in controlling colonization by specific organisms, particularly anaerobes, was investigated. The degree of colonization was estimated from the viable counts in the effluent from the tooth. Interactions between the bacterial species in the multi-culture plaques are discussed. The results are presented in support of the hypothesis that colonization of the teeth by anaerobes depends upon prior growth of aerobes during early plaque formation.