Biofilms of Clostridium species

Why do lactic acid bacteria thrive in chain elongation microbiomes?

Efficient waste management is necessary to transition towards a more sustainable society. An emerging trend is to use mixed culture biotechnology to produce chemicals from organic waste. Insights into the metabolic interactions between community members and their growth characterization are needed to mediate knowledge-driven bioprocess development and optimization. Here, a granular sludge bioprocess for the production of caproic acid through sugar-based chain elongation metabolism was established. Lactic acid and chain-elongating bacteria were identified as the two main functional guilds in the granular community. The growth features of the main community representatives (isolate Limosilactobacillus musocae G03 for lactic acid bacteria and type strain Caproiciproducens lactatifermentans for chain-elongating bacteria) were characterized. The measured growth rates of lactic acid bacteria (0.051 ± 0.005 h-1) were two times higher than those of chain-elongating bacteria (0.026 ± 0.004 h-1), while the biomass yields of lactic acid bacteria (0.120 ± 0.005 g biomass/g glucose) were two times lower than that of chain-elongating bacteria (0.239 ± 0.007 g biomass/g glucose). This points towards differential growth strategies, with lactic acid bacteria resembling that of a r-strategist and chain-elongating bacteria resembling that of a K-strategist. Furthermore, the half-saturation constant of glucose for L. mucosae was determined to be 0.35 ± 0.05 g/L of glucose. A linear trend of caproic acid inhibition on the growth of L. mucosae was observed, and the growth inhibitory caproic acid concentration was predicted to be 13.6 ± 0.5 g/L, which is the highest reported so far. The pre-adjustment of L. mucosae to 4 g/L of caproic acid did not improve the overall resistance to it, but did restore the growth rates at low caproic acid concentrations (1-4 g/L) to the baseline values (i.e., growth rate at 0 g/L of caproic acid). High resistance to caproic acid enables lactic acid bacteria to persist and thrive in the systems intended for caproic acid production. Here, insights into the growth of two main functional guilds of sugar-based chain elongation systems are provided which allows for a better understanding of their interactions and promotes future bioprocess design and optimization.

Clostridioides difficile Biofilm

Clostridioides difficile infection (CDI), previously Clostridium difficile infection, is a symptomatic infection of the large intestine caused by the spore-forming anaerobic, gram-positive bacterium Clostridioides difficile. CDI is an important healthcare-associated disease worldwide, characterized by high levels of recurrence, morbidity, and mortality. CDI is observed at a higher rate in immunocompromised patients after antimicrobial therapy, with antibiotics disrupting the commensal microbiota and promoting C. difficile colonization of the gastrointestinal tract.A rise in clinical isolates resistant to multiple antibiotics and the reduced susceptibility to the most commonly used antibiotic molecules have made the treatment of CDI more complicated, allowing the persistence of C. difficile in the intestinal environment.Gut colonization and biofilm formation have been suggested to contribute to the pathogenesis and persistence of C. difficile. In fact, biofilm growth is considered as a serious threat because of the related antimicrobial tolerance that makes antibiotic therapy often ineffective. This is the reason why the involvement of C. difficile biofilm in the pathogenesis and recurrence of CDI is attracting more and more interest, and the mechanisms underlying biofilm formation of C. difficile as well as the role of biofilm in CDI are increasingly being studied by researchers in the field.Findings on C. difficile biofilm, possible implications in CDI pathogenesis and treatment, efficacy of currently available antibiotics in treating biofilm-forming C. difficile strains, and some antimicrobial alternatives under investigation will be discussed here.

High Prevalence of Multidrug-Resistant, Biofilm-Forming Virulent Clostridium perfringens in Broiler Chicken Retail Points in Northeast India

In light of the significant public health and food safety implications associated with Clostridium perfringens, this study aimed to isolate and characterize C. perfringens in samples obtained from broiler chicken retail points in Meghalaya, northeastern India. A total of 280 samples comprising meat, intestinal contents, water, and hand swabs were processed to detect contamination by C. perfringens. The isolates were subjected to toxinotyping, antimicrobial susceptibility testing, and biofilm-forming ability test. The overall occurrence of C. perfringens was 22.5% (17.74-27.85, 95% CI) with the highest recovery from intestine samples (31%; 22.13-41.03, 95% CI), followed by meat (23%, 15.17-32.49, 95% CI) and water samples (18%, 8.58-31.44, 95% CI). Type A was the predominant toxinotype (71.43%, 58.65-82.11, 95% CI), followed by Type A with beta2 toxin (17.46%, 9.05-29.10, 95% CI), Type C (7.94%, 2.63-17.56, 95% CI), and Type C with beta2 toxin (3.17%, 0.39-11.0, 95% CI). Nearly all (95.24%) isolates were multidrug resistant and 68.25% were biofilm formers. The predominance of multidrug-resistant and virulent Type A and Type C C. perfringens in retail broiler meat and intestines in the tribal-dominated northeastern region of India is of great concern from food safety and public health perspectives.

Review of the Impact of Biofilm Formation on Recurrent Clostridioides difficile Infection

Clostridioides difficile infection (CDI) may recur in approximately 10-30% of patients, and the risk of recurrence increases with each successive recurrence, reaching up to 65%. C. difficile can form biofilm with approximately 20% of the bacterial genome expressed differently between biofilm and planktonic cells. Biofilm plays several roles that may favor recurrence; for example, it may act as a reservoir of spores, protect the vegetative cells from the activity of antibiotics, and favor the formation of persistent cells. Moreover, the expression of several virulence genes, including TcdA and TcdB toxins, has been associated with recurrence. Several systems and structures associated with adhesion and biofilm formation have been studied in C. difficile, including cell-wall proteins, quorum sensing (including LuxS and Agr), Cyclic di-GMP, type IV pili, and flagella. Most antibiotics recommended for the treatment of CDI do not have activity on spores and do not eliminate biofilm. Therapeutic failure in R-CDI has been associated with the inadequate concentration of drugs in the intestinal tract and the antibiotic resistance of a biofilm. This makes it challenging to eradicate C. difficile in the intestine, complicating antibacterial therapies and allowing non-eliminated spores to remain in the biofilm, increasing the risk of recurrence. In this review, we examine the role of biofilm on recurrence and the challenges of treating CDI when the bacteria form a biofilm.

Characterizing the microbiota of cleft lip and palate patients: a comprehensive review

Orofacial cleft disorders, including cleft lip and/or palate (CL/P), are one of the most frequently-occurring congenital disorders worldwide. The health issues of patients with CL/P encompass far more than just their anatomic anomaly, as patients with CL/P are prone to having a high incidence of infectious diseases. While it has been previously established that the oral microbiome of patients with CL/P differs from that of unaffected patients, the exact nature of this variance, including the relevant bacterial species, has not been fully elucidated; likewise, examination of anatomic locations besides the cleft site has been neglected. Here, we intended to provide a comprehensive review to highlight the significant microbiota differences between CL/P patients and healthy subjects in various anatomic locations, including the teeth inside and adjacent to the cleft, oral cavity, nasal cavity, pharynx, and ear, as well as bodily fluids, secretions, and excretions. A number of bacterial and fungal species that have been proven to be pathogenic were found to be prevalently and/or specifically detected in CL/P patients, which can benefit the development of CL/P-specific microbiota management strategies.

Comparative biofilm-forming ability between Clostridioides difficile strains isolated in Latin America and the epidemic NAP1/027 strain

Introduction

One of the challenges in treating Clostridioides difficile infection (CDI) is that the bacterium forms biofilms, a critical virulence mechanism known to promote antibiotic resistance and, as a result, consequently, a higher recurrence of the disease. The goal of this study was to compare the ability of three MLST Clade 2 strains to form a biofilm in vitro: ICC-45 (ribotype SLO231/UK[CE]821), a ST41 toxinotype IXb isolated in Brazil; and two epidemic NAP1/027/ST01 strains: NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica and the reference epidemic strain NAP1/027/ST01 (R20291); and ATCC700057, a non-toxigenic strain.

Methods

The ability of strains to form biofilm was evaluated using crystal violet staining. In addition, samples were stained with the Film Tracer biofilm matrix (Invitrogen®) and the biofilm matrix thickness was measured using confocal microscopy. The matrix architecture was determined using Scanning electron microscop. Confocal microscopy was used to detect the presence of toxin A (tcdA) using an anti-Clostridioides difficile TcdA antibody. The expression of virulence genes (tcdA, tcdB, tcdC, cdtB, spo0A, slpA, cwp66 and cwp84) was examined, as well as the effect of antibiotics metronidazole (MTZ) and vancomycin (VAN) on biofilm growth.

Results

All of the strains tested formed a moderate biofilm with 1.1 <DO_570nm>3.5. After 72h, biofilm biomass of the NAP1/027/ST01 epidemic strains (LIBA5756 and R20291) was significantly higher than ICC-45 and ATCC 700057 biofilms, as confirmed by electron and confocal microscopy. At 120h, the LIBA5756 biofilm biomass decreased compared to other strains. The toxigenic strains R20291 or LIBA 5756 had higher expression of genes tcdA, tcdB, tcdC, cdtA, slpA and spo0A than ICC-45, but there were no significant differences in the expression levels of cdtB, cwp66 and cwp84. In epidemic strains, VAN and MTZ inhibited biofilm formation; however, in the ICC-45 strain, MIC concentrations of VAN and MIC and 4MIC of MTZ did not inhibit biofilm formation.

Conclusion

The three MLST Clade 2 isolated from different rybotipes, two of which were isolated from Latin America, are competent biofilm-forming bacteria, indicating their ability to induce C. difficile infection recurrence, making treatment difficult.

Elucidating the Role of Biofilm-Forming Microbial Communities in Fermentative Biohydrogen Process: An Overview

Amongst the biofuels described in the literature, biohydrogen has gained heightened attention over the past decade due to its remarkable properties. Biohydrogen is a renewable form of H2 that can be produced under ambient conditions and at a low cost from biomass residues. Innovative approaches are continuously being applied to overcome the low process yields and pave the way for its scalability. Since the process primarily depends on the biohydrogen-producing bacteria, there is a need to acquire in-depth knowledge about the ecology of the various assemblages participating in the process, establishing effective bioaugmentation methods. This work provides an overview of the biofilm-forming communities during H2 production by mixed cultures and the synergistic associations established by certain species during H2 production. The strategies that enhance the growth of biofilms within the H2 reactors are also discussed. A short section is also included, explaining techniques used for examining and studying these biofilm structures. The work concludes with some suggestions that could lead to breakthroughs in this area of research.

Electrochemical Control of Biofilm Formation and Approaches to Biofilm Removal

This review deals with microbial adhesion to metal-based surfaces and the subsequent biofilm formation, showing that both processes are a serious problem in the food industry, where pathogenic microorganisms released from the biofilm structure may pollute food and related material during their production. Biofilm exhibits an increased resistance toward sanitizers and disinfectants, which complicates the removal or inactivation of microorganisms in these products. In the existing traditional techniques and modern approaches for clean-in-place, electrochemical biofilm control offers promising technology, where surface properties or the reactions taking place on the surface are controlled to delay or prevent cell attachment or to remove microbial cells from the surface. In this overview, biofilm characterization, the classification of bacteria-forming biofilms, the influence of environmental conditions for bacterial attachment to material surfaces, and the evaluation of the role of biofilm morphology are described in detail. Health aspects, biofilm control methods in the food industry, and conventional approaches to biofilm removal are included as well, in order to consider the possibilities and limitations of various electrochemical approaches to biofilm control with respect to potential applications in the food industry.

Response of a Coastal Microbial Community to Olivine Addition in the Muping Marine Ranch, Yantai

Spreading olivine powder in seawater to enhance alkalinity through weathering reactions has been proposed as a potential solution to control atmospheric CO₂ concentration. Attention has usually been paid to the chemical properties of seawater after the addition of olivine within lab and modeling studies. However, both microbial acclimation and evolution in such manipulated natural environments are often overlooked, yet they are of great importance for understanding the biological consequences of whether olivine addition is a feasible approach to mitigating climate change. In this study, an olivine addition experiment was conducted to investigate variation in bacterial diversity and community composition in the surface and bottom seawater of a representative marine ranch area in the Muping, Yantai. The results show that the composition of the particle-attached microbial community was particularly affected by the application of olivine. The relative abundance of biofilm-forming microbes in particle-attached fraction increased after the addition of olivine, while no significant variation in the free-living bacterial community was observed. Our study suggests that olivine addition would reshape the bacterial community structure, especially in particle-attached microenvironments. Therefore, the risk evaluation of alkalinity enhancement should be further studied before its large-scale application as a potential ocean geoengineering plan.

Gut biofilms: Bacteroides as model symbionts to study biofilm formation by intestinal anaerobes

Bacterial biofilms are communities of adhering bacteria that express distinct properties compared to their free-living counterparts, including increased antibiotic tolerance and original metabolic capabilities. Despite the potential impact of the biofilm lifestyle on the stability and function of the dense community of micro-organisms constituting the mammalian gut microbiota, the overwhelming majority of studies performed on biofilm formation by gut bacteria focused either on minor and often aerobic members of the community or on pathogenic bacteria. In this review, we discuss the reported evidence for biofilm-like structures formed by gut bacteria, the importance of considering the anaerobic nature of gut biofilms and we present the most recent advances on biofilm formation by Bacteroides, one of the most abundant genera of the human gut microbiota. Bacteroides species can be found attached to food particles and colonizing the mucus layer and we propose that Bacteroides symbionts are relevant models to probe the physiology of gut microbiota biofilms.

Membrane bioreactors for syngas permeation and fermentation

Syngas fermentation to biofuels and chemicals is an emerging technology in the biobased economy. Mass transfer is usually limiting the syngas fermentation rate, due to the low aqueous solubilities of the gaseous substrates. Membrane bioreactors, as efficient gas-liquid contactors, are a promising configuration for overcoming this gas-to-liquid mass transfer limitation, so that sufficient productivity can be achieved. We summarize the published performances of these reactors. Moreover, we highlight numerous parameters settings that need to be used for the enhancement of membrane bioreactor performance. To facilitate this enhancement, we relate mass transfer and other performance indicators to the type of membrane material, module, and flow configuration. Hollow fiber modules with dense or asymmetric membranes on which biofilm might form seem suitable. A model-based approach is advocated to optimize their performance.

Clostridium acetobutylicum Biofilm: Advances in Understanding the Basis

Clostridium acetobutylicum is an important industrial platform capable of producing a variety of biofuels and bulk chemicals. Biofilm of C. acetobutylicum renders many production advantages and has been long and extensively applied in fermentation. However, molecular and genetic mechanisms underlying the biofilm have been much less studied and remain largely unknown. Here, we review studies to date focusing on C. acetobutylicum biofilms, especially on its physiological and molecular aspects, summarizing the production advantages, cell physiological changes, extracellular matrix components and regulatory genes of the biofilm. This represents the first review dedicated to the biofilm of C. acetobutylicum. Hopefully, it will deepen our understanding toward C. acetobutylicum biofilm and inspire more research to learn and develop more efficient biofilm processes in this industrially important bacterium.

Evaluating tannery wastewater treatment performance based on physicochemical and microbiological characteristics: An Ethiopian case study

Tanneries are an important industrial sector in Ethiopia; consequently, gaps in wastewater treatment process performance need to be identified as the country increases its emphasis on compliance. A case study was conducted to evaluate physicochemical and microbial water quality at a tannery near Addis Ababa. The treatment process was designed for the following: sulfide oxidation; biological oxygen demand reduction; and chromium removal. While some of Ethiopia's standards for industrial wastewater treatment were met through treatment, effluent COD, sulfide, total nitrogen, and total chromium guidelines were not. 16S rRNA gene analysis was used to evaluate the microbial community composition across the treatment train. The results show that common ruminant phyla were dominant throughout, with Firmicutes and Bacteroidetes comprising 77% to 82% relative abundance. The Firmicutes Clostridium increased consistently in relative abundance with treatment, comprising 39% to 61% of the total bacterial community in the effluent. Improved treatment is needed to meet environmental and public health goals. PRACTITIONER POINTS: Case Study of tannery wastewater treatment in Ethiopia shows ineffective treatment of chemical pollutants. Microbiological pollutants from tannery wastewater systems can introduce agents of importance to public health The microbiological composition of tannery influent, mixed liquor and effluent contains mostly four bacterial phyla lead by Firmicutes. Most pathogenic bacterial genera found in the tannery wastewater treatment system became a decreasing percentage of the total population. Clostridium comprises up to 61% of the effluent bacterial population and deserves further evaluation to better understand the consequences of its dominance.

Biofilm and Spore Formation of Clostridium perfringens and Its Resistance to Disinfectant and Oxidative Stress

Clostridium perfringens is a major human pathogen that causes gastroenteritis via enterotoxin production and has the ability to form spores and biofilms for environmental persistence and disease transmission. This study aimed to compare the disinfectant and environmental resistance properties of C. perfringens vegetative cells and spores in planktonic and sessile conditions, and to examine the nucleotide polymorphisms and transcription under sessile conditions in C. perfringens strains isolated from meat. The sporulation rate of sessile C. perfringens TYJAM-D-66 (cpe+) was approximately 19% at day 5, while those of CMM-C-80 (cpe−) and SDE-B-202 (cpe+) were only 0.26% and 0.67%, respectively, at day 7. When exposed to aerobic conditions for 36 h, TYJAM-D-66, CMM-C-80, and SDE-B-202 vegetative cells showed 1.70 log, 5.36 log, and 5.67 log reductions, respectively. After treatment with sodium hypochlorite, the survival rates of TYJAM-D-66 vegetative cells (53.6%) and spores (82.3%) in biofilms were higher than those of planktonic cells (9.23%). Biofilm- and spore-related genes showed different expression within TYJAM-D-66 (–4.66~113.5), CMM-C-80 (–3.02~2.49), and SDE-B-202 (–5.07~2.73). Our results indicate the resistance of sessile cells and spores of C. perfringens upon exposure to stress conditions after biofilm formation.

Biopolymers modulate microbial communities in municipal organic waste digestion

The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.

Biohydrogen production in a continuous liquid/gas hollow fiber membrane bioreactor: Efficient retention of hydrogen producing bacteria via granule and biofilm formation

The aim of this work was to develop a continuous liquid/gas membrane bioreactor (L/G MBR), i.e. a fermenting module including hollow fibers membrane for L/G separation, for biohydrogen production by dark fermentation. Originally seeded with sludge from a wastewater treatment plant, the L/G MBR underwent a complete stop for eight months. It was then operated without further reseeding. In the present experiment, performed 551 days after the last reseeding, average hydrogen yield of 1.1 ± 0.2 mol per mol glucose added and hydrogen productivity of 135 ± 22 mL/L/h were reached, with acetate and butyrate as the main metabolite products. DNA sequence analysis revealed that Clostridium beijerinckii, Clostridium pasteurianum and Enterobacter sp. were dominant in liquid outlet, in a biofilm on the surface of the hollow fibers and in microbial granules. The L/G MBR has potential for the concentration and the long-term maintenance of an active hydrogen-producing bacterial community without need for reseeding.

Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ

Biofilms are community structures of bacteria enmeshed in a self-produced matrix of exopolysaccharides. The biofilm matrix serves numerous roles, including resilience and persistence, making biofilms a subject of research interest among persistent clinical pathogens of global health importance. Our current understanding of the underlying biochemical pathways responsible for biosynthesis of these exopolysaccharides is largely limited to Gram-negative bacteria. Clostridia are a class of Gram-positive, anaerobic and spore-forming bacteria and include the important human pathogens Clostridium perfringens, Clostridium botulinum and Clostridioides difficile, among numerous others. Several species of Clostridia have been reported to produce a biofilm matrix that contains an acetylated glucan linked to a series of hypothetical genes. Here, we propose a model for the function of these hypothetical genes, which, using homology modelling, we show plausibly encode a synthase complex responsible for polymerization, modification and export of an O-acetylated cellulose exopolysaccharide. Specifically, the cellulose synthase is homologous to that of the known exopolysaccharide synthases in Gram-negative bacteria. The remaining proteins represent a mosaic of evolutionary lineages that differ from the described Gram-negative cellulose exopolysaccharide synthases, but their predicted functions satisfy all criteria required for a functional cellulose synthase operon. Accordingly, we named these hypothetical genes ccsZABHI, for the Clostridial cellulose synthase (Ccs), in keeping with naming conventions for exopolysaccharide synthase subunits and to distinguish it from the Gram-negative Bcs locus with which it shares only a single one-to-one ortholog. To test our model and assess the identity of the exopolysaccharide, we subcloned the putative glycoside hydrolase encoded by ccsZ and solved the X-ray crystal structure of both apo- and product-bound CcsZ, which belongs to glycoside hydrolase family 5 (GH-5). Although not homologous to the Gram-negative cellulose synthase, which instead encodes the structurally distinct BcsZ belonging to GH-8, we show CcsZ displays specificity for cellulosic materials. This specificity of the synthase-associated glycosyl hydrolase validates our proposal that these hypothetical genes are responsible for biosynthesis of a cellulose exopolysaccharide. The data we present here allowed us to propose a model for Clostridial cellulose synthesis and serves as an entry point to an understanding of cellulose biofilm formation among class Clostridia.

Gas gangrene-associated gliding motility is regulated by the Clostridium perfringens CpAL/VirSR system

Clostridium perfringens strains cause a wide variety of human and animal disease, including gas gangrene or myonecrosis. Production of toxins required for myonecrosis, PFO and CPA, is regulated by the C. perfringens Agr-like (CpAL) system via the VirSR two-component system. Myonecrosis begins at the site of infection from where bacteria migrate deep into the host tissue likely using a previously described gliding motility phenotype. We therefore assessed whether gliding motility was under the control of the CpAL/VirSR regulon. The migration rate of myonecrosis-causing C. perfringens strain 13 (S13) was investigated during a 96 h period, including an adaptation phase with bacterial migration (∼1.4 mm/day) followed by a gliding phase allowing bacteria faster migration (∼8.6 mm/day). Gliding required both an intact CpAL system, and signaling through VirSR. Mutants lacking ΔagrB, or ΔvirR, were impaired for onward gliding while a complemented strain S13ΔagrB/pTS1303 had the gliding phenotype restored. Gene expression studies revealed upregulated transcription of pili genes (pilA1, pilA2 and pilT) whose encoded proteins were previously found to be required for gliding motility and CpAL/VirSR-regulated pfoA and cpa toxin genes. Compared to S13, transcription of cpa and pfoA significantly decreased in S13ΔagrB, or S13ΔvirR, strains but not that of pili genes. Further experiments demonstrated that mutants S13ΔpfoA and S13Δcpa migrated at the same rate as S13 wt. We demonstrated that CpAL/VirSR regulates C. perfringens gliding motility and that gliding bacteria have an increased transcription of toxin genes involved in myonecrosis.

Effect of temperature and surfactant on biomass growth and higher-alcohol production during syngas fermentation by Clostridium carboxidivorans P7

Hexanol–butanol–ethanol fermentation from syngas by Clostridium carboxidivorans P7 is a promising route for biofuel production. However, bacterial agglomeration in the culture of 37 °C severely hampers the accumulation of biomass and products. To investigate the effect of culture temperature on biomass growth and higher-alcohol production, C. carboxidivorans P7 was cultivated at both constant and two-step temperatures in the range from 25 to 37 °C. Meanwhile, Tween-80 and saponin were screened out from eight surfactants to alleviate agglomeration at 37 °C. The results showed that enhanced higher-alcohol production was contributed mainly by the application of two-step temperature culture rather than the addition of anti-agglomeration surfactants. Furthermore, comparative transcriptome revealed that although 37 °C promoted high expression of genes involved in the Wood–Ljungdahl pathway, genes encoding enzymes catalyzing acyl-condensation reactions associated with higher-alcohol production were highly expressed at 25 °C. This study gained greater insight into temperature-effect mechanism on syngas fermentation by C. carboxidivorans P7.

Temperature-regulated heterogeneous extracellular matrix gene expression defines biofilm morphology in Clostridium perfringens

Cells in biofilms dynamically adapt to surrounding environmental conditions, which alters biofilm architecture. The obligate anaerobic pathogen Clostridium perfringens shows different biofilm structures in different temperatures. Here we find that the temperature-regulated production of extracellular polymeric substance (EPS) is necessary for morphological changes in biofilms. We identify BsaA proteins as an EPS matrix necessary for pellicle biofilm formation at lower temperature and find that extracellularly secreted BsaA protein forms filamentous polymers. We show that sipW-bsaA operon expression is bimodal, and the EPS-producing population size is increased at a lower temperature. This heterogeneous expression of the EPS gene requires a two-component system. We find that EPS-producing cells cover EPS-nonproducing cells attaching to the bottom surface. In the deletion mutant of pilA2, encoding a type IV pilin, the EPS gene expression is ON in the whole population. This heterogeneity is further regulated by the cleavage of the pilA2 mRNA by RNase Y, causing temperature-responsive EPS expression in biofilms. As temperature is an environmental cue, C. perfringens may modulate EPS expression to induce morphological changes in biofilm structure as a strategy for adapting to interhost and external environments.

Impacts of biofilms on the conversion of cellulose

Abstract

Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms—matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature—have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted.

Key Points

Multispecies biofilms enable efficient lignocellulose destruction in the biosphere.

Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms.

Fungal biofilms immobilize enzymes and substrates in an external digestion system.

Surface attached cultures typically show higher expression of cellulolytic enzymes.

Inhibitory effect of fidaxomicin on biofilm formation in Clostridioides difficile

Clostridioides difficile infection results from a disturbance of the normal microbial flora of the colon, allowing proliferation of C. difficile and toxin production by toxigenic strains. Fidaxomicin, a macrocyclic antibiotic that prevents RNA synthesis in C. difficile and inhibits spore formation, toxin production, and cell proliferation, is clinically effective in treating C. difficile infection. As recent studies have suggested that biofilm formation influences C. difficile colonization and infection in the colon, we undertook the present study to determine the effects of fidaxomicin on C. difficile biofilm formation. Sub-minimum inhibitory concentrations (MICs) of fidaxomicin inhibited biofilm formation by C. difficile UK027 and delayed planktonic growth. Sub-MICs of vancomycin did not inhibit biofilm formation or affect planktonic growth. In C. difficile UK027 exposed to sub-MICs of fidaxomicin, mRNA expression of biofilm-related flagellin gene fliC was slightly increased compared with that of other biofilm-related genes (pilA1, cwp84, luxS, dccA, and spo0A). In conclusion, this study indicates that sub-MICs of fidaxomicin inhibit C. difficile UK027 biofilm formation by influencing cell growth and fliC transcription.

The Ser/Thr Kinase PrkC Participates in Cell Wall Homeostasis and Antimicrobial Resistance in Clostridium difficile

Clostridium difficile is the leading cause of antibiotic-associated diarrhea in adults. During infection, C. difficile must detect the host environment and induce an appropriate survival strategy. Signal transduction networks involving serine/threonine kinases (STKs) play key roles in adaptation, as they regulate numerous physiological processes. PrkC of C. difficile is an STK with two PASTA domains. We showed that PrkC is membrane associated and is found at the septum. We observed that deletion of prkC affects cell morphology with an increase in mean size, cell length heterogeneity, and presence of abnormal septa. A ΔprkC mutant was able to sporulate and germinate but was less motile and formed more biofilm than the wild-type strain. Moreover, a ΔprkC mutant was more sensitive to antimicrobial compounds that target the cell envelope, such as the secondary bile salt deoxycholate, cephalosporins, cationic antimicrobial peptides, and lysozyme. This increased susceptibility was not associated with differences in peptidoglycan or polysaccharide II composition. However, the ΔprkC mutant had less peptidoglycan and released more polysaccharide II into the supernatant. A proteomic analysis showed that the majority of C. difficile proteins associated with the cell wall were less abundant in the ΔprkC mutant than the wild-type strain. Finally, in a hamster model of infection, the ΔprkC mutant had a colonization delay that did not significantly affect overall virulence.

Distinct microbially induced concrete corrosion at the tidal region of reinforced concrete sewers

Microbially induced concrete corrosion (MICC) is a major deterioration affecting sewers worldwide. MICC is not uniform on sewer inner walls and often occurs at hot spots such as crown and tidal regions, which are critical to determine sewer service life. Especially, concrete corrosion in tidal regions is complicated due to the fluctuation of wastewater levels and the hydraulic scouring effects. The traditional methodology of corrosion monitoring also limits the study of the tidal corrosion. In this study, by using a combination of various advanced mineral analytical techniques and culture-independent 16S rRNA gene amplicon sequencing, the development of corrosion, the formation of corrosion products and the variation of microbial communities in tidal regions were investigated systematically. The physical-chemical characteristics in tidal regions varied with the distance from the wastewater surface. Above the wastewater, more severe corrosion was detected with a closer distance to wastewater, producing gypsum as the major corrosion products. The microbial succession in tidal regions occurred, with the coexistence of conventional autotrophic SOB and acidophilic heterotrophic bacteria initially, and shifting to the predominant colonization of Mycobacterium when pH reached around 1. The heterotrophic bacteria, i.e. Mycobacterium and Bacillus, were likely responsible for the observed corrosion due to the potential capability in generating sulfuric acid. The applications of advanced mineral and microbial analytical techniques were demonstrated effective in improving the understanding of concrete sewer corrosion.

Clostridium acetobutylicum grows vegetatively in a biofilm rich in heteropolysaccharides and cytoplasmic proteins

BACKGROUND

Biofilms are cell communities wherein cells are embedded in a self-produced extracellular polymeric substances (EPS). The biofilm of Clostridium acetobutylicum confers the cells superior phenotypes and has been extensively exploited to produce a variety of liquid biofuels and bulk chemicals. However, little has been known about the physiology of C. acetobutylicum in biofilm as well as the composition and biosynthesis of the EPS. Thus, this study is focused on revealing the cell physiology and EPS composition of C. acetobutylicum biofilm.

RESULTS

Here, we revealed a novel lifestyle of C. acetobutylicum in biofilm: elimination of sporulation and vegetative growth. Extracellular polymeric substances and wire-like structures were also observed in the biofilm. Furthermore, for the first time, the biofilm polysaccharides and proteins were isolated and characterized. The biofilm contained three heteropolysaccharides. The major fraction consisted of predominantly glucose, mannose and aminoglucose. Also, a great variety of proteins including many non-classically secreted proteins moonlighting as adhesins were found considerably present in the biofilm, with GroEL, a S-layer protein and rubrerythrin being the most abundant ones.

CONCLUSIONS

This study evidenced that vegetative C. acetobutylicum cells rather than commonly assumed spore-forming cells were essentially the solvent-forming cells. The abundant non-classically secreted moonlighting proteins might be important for the biofilm formation. This study provides the first physiological and molecular insights into C. acetobutylicum biofilm which should be valuable for understanding and development of the biofilm-based processes.

Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture

Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA₁, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA₁ in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA₁. dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA₁. Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.

Clostridium difficile forms variable biofilms on abiotic surface

Clostridium difficile can form biofilms. Thirty-seven strains were characterized for their ability to form a biofilm, adhesion on an inert surface and hydrophobicity. No correlation between the ability to form a biofilm and the strain virulence was highlighted. However, non-motile strains were not able to form a high biofilm.

Comparative transcriptomic analysis of Clostridium perfringens biofilms and planktonic cells

Clostridium perfringens is an opportunistic pathogen that can cause food poisoning in humans and various enterotoxaemias in animal species. Recently, C. perfringens was shown to form biofilms, a structured community of bacterial cells enclosed in a self-produced extracellular matrix. However, very little is known on the subject and no information is available on gene expression in C. perfringens biofilms. To gain insights into the differences between free-living C. perfringens cells and those in biofilms, we used RNA sequencing. In total, 25.7% of genes showed differential expression in the two growth modes; about 12.8% of genes were up-regulated and about 12.9% were down-regulated in biofilms. We show that 772 genes were significantly differentially expressed between biofilms and planktonic cells from the supernatant of biofilms. Genes that were down-regulated in biofilm cells, relative to planktonic cells, included those involved in virulence, energy production, amino acid, nucleotide and carbohydrate metabolism, and in translation and ribosomal structure. Genes up-regulated in biofilm cells were mainly involved in amino acid and carbohydrate metabolism, transcription, inorganic ion metabolism and in defence mechanisms. This study provides new insights into the transcriptomic response of C. perfringens during biofilm formation.

Surviving Between Hosts: Sporulation and Transmission

To survive adverse conditions, some bacterial species are capable of developing into a cell type, the "spore," which exhibits minimal metabolic activity and remains viable in the presence of multiple environmental challenges. For some pathogenic bacteria, this developmental state serves as a means of survival during transmission from one host to another. Spores are the highly infectious form of these bacteria. Upon entrance into a host, specific signals facilitate germination into metabolically active replicating organisms, resulting in disease pathogenesis. In this article, we will review spore structure and function in well-studied pathogens of two genera, Bacillus and Clostridium, focusing on Bacillus anthracis and Clostridium difficile, and explore current data regarding the lifestyles of these bacteria outside the host and transmission from one host to another.

Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis

The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na⁺ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.

Assessing Methanobrevibacter smithii and Clostridium difficile as not conventional faecal indicators in effluents of a wastewater treatment plant integrated with sludge anaerobic digestion

Wastewater treatment plants (WWTP) are an important source of surface water contamination by enteric pathogens, affecting the role of environmental water as a microbial reservoir. We describe the release to the environment of certain anaerobes of human and environmental concern. The work was focused on emerging microbial targets. They are tracing, by RT-qPCR, on WWTP effluents, both liquid and solid, when an anaerobic digestion step is included. The focus is placed on Clostridium spp. with the specific quantification of Clostridium perfringens, as typical bioindicator, and Clostridium difficile, as emerging pathogen not only confined into nosocomial infection. Moreover methanogens were quantified for their involvement in the anaerobic digestion, and in particular on Methanobrevibacter smithii as major methanogenic component of the human gut microbiome and as not conventional faecal indicator. In the water samples, a reduction, statistically significant, in all microbial targets was observed (p < 0.01), 2 log for the total bacteria, 1.4 log for the Clostridium spp. and M. smithii, 1 log for total methanogens, C. perfringens and C. difficile. The AD process contribute to a significant change in microbial levels into the sludge for total bacteria and total methanogens (p < 0.01), both when the input sludge are primary and secondary, while for the presence of Clostridium spp. and C. difficile there was not a significant change. The produced data are innovative showing which is the diffusion of such anaerobic microorganisms throughout the WWTP and opening a discussion on the implementation of possible techniques for a more efficient microbial removal from effluents, particularly bio-solids, to reduce the potential release of pathogens into the environment.

Subinhibitory concentrations of metronidazole increase biofilm formation in Clostridium difficile strains

Resistance mechanism to metronidazole is still poorly understood, even if the number of reports on Clostridium difficile strains with reduced susceptibility to this antibiotic is increasing. In this study, we investigated the ability of the C. difficile strains 7032994, 7032985 and 7032989, showing different susceptibility profiles to metronidazole but all belonging to the PCR ribotype 010, to form biofilm in vitro in presence and absence of subinhibitory concentrations of metronidazole. The quantitative biofilm production assay performed in presence of metronidazole revealed a significant increase in biofilm formation in both the susceptible strain 7032994 and the strain 7032985 exhibiting a reduced susceptibility to this antibiotic, while antibiotic pressure did not affect the biofilm-forming ability of the stable-resistant strain 7032989. Moreover, confocal microscopy analysis showed an abundant biofilm matrix production by the strains 7032994 and 7032885, when grown in presence of metronidazole, but not in the stable-resistant one. These results seem to demonstrate that subinhibitory concentrations of metronidazole are able to enhance the in vitro biofilm production of the above-mentioned PCR ribotype 010 C. difficile strains, susceptible or with reduced susceptibility to this antibiotic, suggesting a possible role of biofilm formation in the multifactorial mechanism of metronidazole resistance developed by C. difficile.

The Clostridium difficile Protease Cwp84 Modulates both Biofilm Formation and Cell-Surface Properties

Clostridium difficile is responsible for 15-20% of antibiotic-associated diarrheas, and nearly all cases of pseudomembranous colitis. Among the cell wall proteins involved in the colonization process, Cwp84 is a protease that cleaves the S-layer protein SlpA into two subunits. A cwp84 mutant was previously shown to be affected for in vitro growth but not in its virulence in a hamster model. In this study, the cwp84 mutant elaborated biofilms with increased biomass compared with the parental strain, allowing the mutant to grow more robustly in the biofilm state. Proteomic analyses of the 630Δerm bacteria growing within the biofilm revealed the distribution of abundant proteins either in cell surface, matrix or supernatant fractions. Of note, the toxin TcdA was found in the biofilm matrix. Although the overall proteome differences between the cwp84 mutant and the parental strains were modest, there was still a significant impact on bacterial surface properties such as altered hydrophobicity. In vitro and in vivo competition assays revealed that the mutant was significantly impaired for growth only in the planktonic state, but not in biofilms or in vivo. Taken together, our results suggest that the phenotypes in the cwp84 mutant come from either the accumulation of uncleaved SlpA, or the ability of Cwp84 to cleave as yet undetermined proteins.