A multispecies biofilm model

Using a continuum approach and observing conservation principles, an analytical mathematical model of microbial interaction in biofilms was developed. The model predicts changes in biofilm thickness and describes the dynamics and spatial distribution of microbial species and substrates in the film. It allows for biomass detachment due to shear stress and sloughing, external mass transfer limitations, as well as variations in substrate concentrations in the bulk liquid. A computer implementation of the model is provided using an example of heterotrophicautotrophic competition to illustrate how the observed phenomena can be numerically reproduced and indicating how they might affect overall biofilm performance.     

c-di-AMP调控细菌生物被膜的形成

细菌生物被膜是细菌持续性致病的重要机制。研究细菌生物被膜的形成和发展可为顽固性细菌感染防治提供新的思路与策略。环二腺苷酸c-di-AMP(Cyclic diadenosine monophosphate)是继c-di-GMP之后在细菌中新发现的一种核苷酸第二信使分子。研究发现,c-di-AMP参与调节细菌多种生理功能,包括细菌生长代谢、生物被膜形成、细胞壁的合成以及细菌毒力因子等。本文综述了c-di-AMP参与调控细菌生物被膜形成的不同方式及其分子机制。鉴于c-di-AMP在调控细菌生物被膜中的重要性,其可作为抗细菌生物被膜感染新药研发的潜在靶点。     

Evolving concepts in biofilm infections

Several pathogens associated with chronic infections, including Pseudomonas aeruginosa in cystic fibrosis pneumonia, Haemophilus influenzae and Streptococcus pneumoniae in chronic otitis media, Staphylococcus aureus in chronic rhinosinusitis and enteropathogenic Escherichia coli in recurrent urinary tract infections, are linked to biofilm formation. Biofilms are usually defined as surface-associated microbial communities, surrounded by an extracellular polymeric substance (EPS) matrix. Biofilm formation has been demonstrated for numerous pathogens and is clearly an important microbial survival strategy. However, outside of dental plaques, fewer reports have investigated biofilm development in clinical samples. Typically biofilms are found in chronic diseases that resist host immune responses and antibiotic treatment and these characteristics are often cited for the ability of bacteria to persist in vivo . This review examines some recent attempts to examine the biofilm phenotype in vivo and discusses the challenges and implications for defining a biofilm phenotype.     

Correlation network analysis applied to complex biofilm communities

The complexity of the human microbiome makes it difficult to reveal organizational principles of the community and even more challenging to generate testable hypotheses. It has been suggested that in the gut microbiome species such as Bacteroides thetaiotaomicron are keystone in maintaining the stability and functional adaptability of the microbial community. In this study, we investigate the interspecies associations in a complex microbial biofilm applying systems biology principles. Using correlation network analysis we identified bacterial modules that represent important microbial associations within the oral community. We used dental plaque as a model community because of its high diversity and the well known species-species interactions that are common in the oral biofilm. We analyzed samples from healthy individuals as well as from patients with periodontitis, a polymicrobial disease. Using results obtained by checkerboard hybridization on cultivable bacteria we identified modules that correlated well with microbial complexes previously described. Furthermore, we extended our analysis using the Human Oral Microbe Identification Microarray (HOMIM), which includes a large number of bacterial species, among them uncultivated organisms present in the mouth. Two distinct microbial communities appeared in healthy individuals while there was one major type in disease. Bacterial modules in all communities did not overlap, indicating that bacteria were able to effectively re-associate with new partners depending on the environmental conditions. We then identified hubs that could act as keystone species in the bacterial modules. Based on those results we then cultured a not-yet-cultivated microorganism, Tannerella sp. OT286 (clone BU063). After two rounds of enrichment by a selected helper (Prevotella oris OT311) we obtained colonies of Tannerella sp. OT286 growing on blood agar plates. This system-level approach would open the possibility of manipulating microbial communities in a targeted fashion as well as associating certain bacterial modules to clinical traits (e.g.: obesity, Crohn's disease, periodontal disease, etc).     

The biofilm matrix--an immobilized but dynamic microbial environment

The biofilm matrix is a dynamic environment in which the component microbial cells appear to reach homeostasis and are optimally organized to make use of all available nutrients. The major matrix components are microbial cells, polysaccharides and water, together with excreted cellular products. The matrix therefore shows great microheterogeneity, within which numerous microenvironments can exist. Although exopolysaccharides provide the matrix framework, a wide range of enzyme activities can be found within the biofilm, some of which will greatly affect structural integrity and stability.     

Microbial landscapes: new paths to biofilm research

It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms.     

Influence of abrasion on biofilm detachment: evidence for stratification of the biofilm

The objective of this paper was to understand the detachment of multispecies biofilm caused by abrasion. By submitting a biofilm to different abrasion strengths (collision of particles), stratification of biofilm cohesion could be highlighted and related to stratification of biofilm bacterial communities using the PCR-SSCP fingerprint method. The biofilm comprised a thick top layer, weakly cohesive and composed of one dominant species, and a thin basal layer, strongly cohesive and composed of a more diverse population. These observations suggest that microbial composition of biofilms may be an important parameter in understanding biofilm detachment.     

Bioengineering report: Fouling biofilm development: A process analysis

Biofilm development at a surface is the net result of several physical, chemical, and microbial processes including the following: (1)transport of dissolved and particulate matter from the bulk fluid to the surface; (2) firm microbial cell attachment to the surface; (3) microbial transformations (growth, reproduction, etc.) within the biofilm resulting in production of organic matter; (4) partial detachment of the biofilm due primarily to fluid shear stress. This report presents a framework for analyzing the interrelated processes contributing to biofilm development. Some of the available rate and composition data are presented so that the relative process rates can be compared.     

Molecular analysis of shower curtain biofilm microbes

Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as "soap scum," which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the alpha-group of proteobacteria, mainly Sphingomonas spp. and Methylobacterium spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.     

Managing microbial communities in membrane biofilm reactors

Membrane biofilm reactors (MBfRs) deliver gaseous substrates to biofilms that develop on the outside of gas-transfer membranes. When an MBfR delivers electron donors hydrogen (H₂) or methane (CH₄), a wide range of oxidized contaminants can be reduced as electron acceptors, e.g., nitrate, perchlorate, selenate, and trichloroethene. When O₂ is delivered as an electron acceptor, reduced contaminants can be oxidized, e.g., benzene, toluene, and surfactants. The MBfR’s biofilm often harbors a complex microbial community; failure to control the growth of undesirable microorganisms can result in poor performance. Fortunately, the community’s structure and function can be managed using a set of design and operation features as follows: gas pressure, membrane type, and surface loadings. Proper selection of these features ensures that the best microbial community is selected and sustained. Successful design and operation of an MBfR depends on a holistic understanding of the microbial community’s structure and function. This involves integrating performance data with omics results, such as with stoichiometric and kinetic modeling.

     

Biodegradation of acetonitrile by adapted biofilm in a membrane-aerated biofilm reactor

A membrane-aerated biofilm reactor (MABR) was developed to degrade acetonitrile (ACN) in aqueous solutions. The reactor was seeded with an adapted activated sludge consortium as the inoculum and operated under step increases in ACN loading rate through increasing ACN concentrations in the influent. Initially, the MABR started at a moderate selection pressure, with a hydraulic retention time of 16 h, a recirculation rate of 8 cm/s and a starting ACN concentration of 250 mg/l to boost the growth of the biofilm mass on the membrane and to avoid its loss by hydraulic washout. The step increase in the influent ACN concentration was implemented once ACN concentration in the effluent showed almost complete removal in each stage. The specific ACN degradation rate achieved the highest at the loading rate of 101.1 mg ACN/g-VSS h (VSS, volatile suspended solids) and then declined with the further increases in the influent ACN concentration, attributed to the substrate inhibition effect. The adapted membrane-aerated biofilm was capable of completely removing ACN at the removal capacity of up to 21.1 g ACN/m² day, and generated negligible amount of suspended sludge in the effluent. Batch incubation experiments also demonstrated that the ACN-degrading biofilm can degrade other organonitriles, such as acrylonitrile and benzonitrile as well. Denaturing gradient gel electrophoresis studies showed that the ACN-degrading biofilms contained a stable microbial population with a low diversity of sequence of community 16S rRNA gene fragments. Specific oxygen utilization rates were found to increase with the increases in the biofilm thickness, suggesting that the biofilm formation process can enhance the metabolic degradation efficiency towards ACN in the MABR. The study contributes to a better understanding in microbial adaptation in a MABR for biodegradation of ACN. It also highlights the potential benefits in using MABRs for biodegradation of organonitrile contaminants in industrial wastewater.     

Leitbakteria of microbial biofilm communities causing occlusion of biliary stents

Biliary stents inserted to relieve obstructive jaundice caused by biliary or pancreatic malignancies inevitably become occluded by microbial growth in the form of diverse microbial community biofilms. The scarce information available on these communities is based on cultivation methods, but such methods usually provide distorted overviews of community composition, so commonalities and differences in biliary stent communities are uncertain. We extracted DNA and RNA from the microbial communities of 11 biliary stents explanted from nine patients in hospitals from two different countries, amplified 16S rRNA and rDNA sequences, analysed the amplicons by the single-strand conformation polymorphism (SSCP) method, and sequenced and deduced phylogenetic assignments of the major amplicons representing the major biofilm community members. We used a Modified Robbins Device (MRD) to study de novo development of a stent biofilm from a patient stent microbial community. Single-strand conformation polymorphism fingerprinting revealed the same six abundant bacterial species, here designated Leitbakteria, namely Klebsiella pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, Enterobacter aerogenes, and two unculturable bacteria distantly related to E. coli and Shigella sonnei, in all of the stent biofilm communities. In the experimental biliary stent system, a sequential colonization of the stent surface was observed, with P. aeruginosa being the pioneer colonizer, followed by K. pneumoniae and one of the unculturable Leitbakteria, followed by the remainder of the community. The overview of microbial biofilm communities of biliary stents gained by the use of culture-independent methods revealed new unculturable bacteria as major members of biliary stent biofilms, and the diversity of the abundant members of the stent biofilms is considerably lower than suggested from earlier studies based on cultivation methods, and that communities from different stents from different patients in different countries are remarkably similar and have similar major members, the stent Leitbakteria.     

Biodiversity and species competition regulate the resilience of microbial biofilm community

The relationship between biodiversity and ecosystem stability is poorly understood in microbial communities. Biofilm communities in small bioreactors called microbial electrolysis cells (MEC) contain moderate species numbers and easy tractable functional traits, thus providing an ideal platform for verifying ecological theories in microbial ecosystems. Here, we investigated the resilience of biofilm communities with a gradient of diversity, and explored the relationship between biodiversity and stability in response to a pH shock. The results showed that all bioreactors could recover to stable performance after pH disturbance, exhibiting a great resilience ability. A further analysis of microbial composition showed that the rebound of Geobacter and other exoelectrogens contributed to the resilient effectiveness, and that the presence of Methanobrevibacter might delay the functional recovery of biofilms. The microbial communities with higher diversity tended to be recovered faster, implying biofilms with high biodiversity showed better resilience in response to environmental disturbance. Network analysis revealed that the negative interactions between the two dominant genera of Geobacter and Methanobrevibacter increased when the recovery time became longer, implying the internal resource or spatial competition of key functional taxa might fundamentally impact the resilience performances of biofilm communities. This study provides new insights into our understanding of the relationship between diversity and ecosystem functioning.     

Electrical conductivity in a mixed-species biofilm

Geobacter sulfurreducens can form electrically conductive biofilms, but the potential for conductivity through mixed-species biofilms has not been examined. A current-producing biofilm grown from a wastewater sludge inoculum was highly conductive with low charge transfer resistance even though microorganisms other than Geobacteraceae accounted for nearly half the microbial community.     

Detachment of multi species biofilm in circulating fluidized bed bioreactor

In this study, the detachment rates of various microbial species from the aerobic and anoxic biofilms in a circulating fluidized bed bioreactor (CFBB) with two entirely separate aerobic and anoxic beds were investigated. Overall detachment rate coefficients for biomass, determined on the basis of volatile suspended solids (VSS), glucose and protein as well as for specific microbial groups, i.e., for nitrifiers, denitrifiers, and phosphorous accumulating organisms (PAOs), were established. Biomass detachment rates were found to increase with biomass attachment on carrier media in both beds. The detachment rate coefficients based on VSS were significantly affected by shear stress, whereas for protein, glucose and specific microbial groups, no significant effect of shear stress was observed. High detachment rates were observed for the more porous biofilm structure. The presence of nitrifiers in the anoxic biofilm and denitrifiers in the aerobic biofilm was established by the specific activity measurements. Detachment rates of PAOs in aerobic and anoxic biofilms were evaluated.     

持留菌及其对微生物膜的耐受性影响研究进展

持留菌（persisters）是细菌种群中所占比例不到0.1%的一类特殊亚群,具有与种群内普通菌、抗性突变菌所不同的特征,其形成机制复杂,不易分离培养.持留菌可通过“休眠-生长-增殖”应对逆境的胁迫,维持自身生存和菌体结构稳定,在生物膜的多药耐受性与多金属耐性中发挥着重要作用,对于维持微生物群落结构稳定具有重要意义.本文从持留菌的研究历程、特点、基因调控机制及其对微生物膜的耐药性与多金属耐性的影响等方面进行了综述,并对今后的研究方向进行了展望.     

基于微流控的生物被膜研究进展及口腔微生态系统应用展望

口腔是人体最重要的微生物储藏库之一,这些微生物通常以生物被膜的形式稳定地黏附于口腔内粘膜及牙齿表面,在病理条件下则可以深入髓腔及牙槽骨内,成为龋病、根尖周炎、牙周病等常见口腔疾病的主要病因,甚至与许多全身性疾病密切相关。在人类口腔微生态系统中,微生物种类繁多,生物被膜的构成及相互作用关系复杂,目前对其认识还十分有限;此外,在宿主免疫、口腔内外多种理化因素的调控下,生物被膜还可以出现不同的表型及生物特性,因此对其致病机制的研究也具有挑战性。微流控技术作为一种能够灵活操控微尺度流体的技术,不仅能够精准模拟理化微环境,还能够进行高通量可视化的分析,在生命分析化学及生物被膜的研究方面已经展现出显著优势,在口腔微生态系统研究中具有广阔的应用前景。本文将回顾近期微流控技术在生物被膜方面的研究进展,并结合口腔微生态系统中生物被膜研究的关键问题对微流控技术的应用做系统阐述和展望。     

Characterization of a sulfide-oxidizing biofilm developed in a packed-column reactor.

The potential of microbial mats to develop sulfide-oxidizing biofims was explored. A bioreactor specially designed for the treatment of sulfide-containing effluents was inoculated with a microbial-mat sample, and a complex microbial biofilm with sulfide-oxidation activity developed. The microbial composition of the biofilm was studied by pigment, microscopy, and 16S rRNA gene analyses. Purple sulfur bacteria and diatoms were observed by microscopy, chlorophyll a and bacteriochlorophyll a were detected in the pigment analysis, and high genetic diversity was found in the 16S rRNA gene library. Specialized anaerobic sulfur oxidizers (i.e., phototrophic purple and green sulfur bacteria) dominated the library. Aerobic phototrophs (diatoms) also developed and the oxygen produced allowed the growth of aerobic sulfide oxidizers, such as Thiomicrospira-like spp. Cyanobacteria, which are significant organisms in natural microbial mats, did not develop in the reactor but unexpected uncultured members from the Epsilonproteobacteria developed profusely. Moreover, a variety of more minor organisms, such as members of the Cytophaga-Flavobacterium-Bacteroides (CFB) and purple non-sulfur bacteria (Roseospirillum sp.), were also present. The results showed that a complex community with high genetic and metabolic diversity, including many uncultured organisms, can develop in a laboratory-scale reactor.     

牙菌斑生物膜的形成与控制

牙菌斑生物膜是附着于牙釉质表面,由复杂的微生物群落构成的一种聚集体。牙菌斑生物膜的形成与生长对口腔健康有着直接或间接的影响,许多研究证实口腔疾病如龋齿和牙周病都与细菌的积累及牙菌斑的形成有关。在牙菌斑生物膜形态建成过程中,牙齿表面最初的定殖菌对生物膜的微生物组成和结构至关重要,这些初级定殖菌决定了后续与之结合形成共生体的微生物种类和数量。不同的微生物组成可能在与生物膜形成相关的口腔病理状况中发挥不同的作用。因此,本文就牙菌斑生物膜的生长及控制进行综述,介绍其微生物的早期定殖和成熟过程、以及通过物理和化学方法对牙菌斑生物膜的控制,以期为了解牙菌斑生物膜的形成机制及相关口腔疾病的预防和治疗提供有价值的参考。