Ebooks

It is heartening to note that a book entitled ‘Biofilms” has been authored by Dr. Renu Agrawal which aims at bringing awareness on biofilms. A biofilm is an assemblage of microbial cells enclosed in an extracellular polymeric matrix. The book starts with the introduction of biofilms, the ways microbes form communities and adhere to the surfaces and are resistant to many antibiotics. The book deals with the progress made on the various aspects of biofilms. The book has been divided into 11 chapters. Chapter two deals with biofilm formation in foods and what can cause cross-contamination in food products. The sub sections discuss biofilms in agriculture, quorum sensing and how trophic-mediated communication are utilized by microbial communities for improving agricultural productivity. Biofilms in soil and plant health has elaborated on the membrane antifouling methods and alternatives:ultrasound approach. Biofilms in fruits and vegetables discusses on the contact surfaces of the biofilms and where they stay during food processing. It describes how the contamination could take place during harvesting, transport, processing, distribution or even while marketing. There are problems due to large consumption of seafoods which has resulted in a number of diseases around the globe. This has been well discussed by the author and a subsection has been devoted for this. Milk has some pathogenic bacteria which can adhere on stainless steel surfaces in the production chain and can form biofilms in milk storage tanks and also in milk processing lines. The book covers the biofilms in dairy and milk products in depth. The use of disinfectant agents and their efficiency has been explained well. Another serious problem of biofilms is in the meat industry, 

There are many bacteria and fungi which produce biofilms. These are made up of living, reproducing microorganisms. These microbes form communities and adhere tightly to the surfaces and are resistant to many antibiotics. Many pathogenic microorganisms form biofilms which are difficult to be removed and are harmful.Such microbial colonies produce an extracellular polymeric substance (EPS) to protect them. The dental plaque was the first documented evidence of microbial biofilms. When such microorganisms get a moist environment they attach themselves to any object and reproduce forming an attachment by secreting a slimy, glue-like substance. It is possible with metals, plastics, natural materials, medical implants, kitchen counters, contact lenses, walls of a hot tub or swimming pool. Initially it was the investigation of many scientists to show the presence of biofilms Beneficial effects of biofilms have also been shown (Rosche et al., 2009) especially in agriculture (Bogino et al., 2013; Berlanga and Guerrero, 2016) where it can be utilized as a biological control agents. They are used as biofertilizers to enhance crop production (Timmusk et al., 2017), hazardous pollutants can be removed (Irankhah et al., 2019). 

Microbial life abounds on a solid substrate. Water and some nutrients are sufficient to allow the microbial construction called biofilm. Biofilm-associated infections (BAI) can enhance chronic infections in which the bacterial pathogens can persist causing cross-contamination of the food products. Giaouris et al. (2014) worked on the meat processing and biofilm formation by foodborne bacteria. Work on seafoods has been well worked by Mizan et al. (2015). Habimana et al. (2010) studied them in feed industry on Salmonella versus host resident flora strains. Lin et al. (2017) have studied the characteristics of some food borne pathogens. In a study by Rao et al. (2020) cold atmospheric plasma can be a solution to prevent biofilms.Ferriol-Gonzalez et al. (2020) worked out that bacteriophages can be helpful to remove biofims. According to Przekwas et al. (2020) in early stage of growth of the biofilm use of ascorbic acid can be helpful for the removal of biofilms. Apples can be protected from pathogenic bacteria by protecting them using harmless bacteria. It leads towards the development of alternative foodborne-pathogen-control strategies. Listeria monocytogenes is a big concern in the NE part of India.

Biofilms play an important part in biotechnology, immunology, biofouling and biodeterioration (Fleming and Wingender, 2001; Dunne, 2002). When the pathogenic cells adhere to the surface, it has been found that the transcription of the EPS genes get stimulated (Dunne, 2002). If EPS gene expression are monitored it can provide a good understanding of biofilm phenotypes (Allison and Sutherland, 1997; Helm and Naumann, 1995; Petersen et al., 2005). EPS serves many functions. It also enables the bacteria to capture nutrients (Pontefract,1991).The formation of biofilm goes through a mechanism which is different from species to species. Even the matrix thickness can be different from 0.2 to 1.0pm depending on the species and doubling time of the cells as thickness of 10 to 30 nm has been found in some bacteria species (Sleytr,1997). The cells secrete polysaccharides, proteins, nucleic acids and glycoproteins. Adherence on solid surfaces by microorganisms is a very complicated process that depends mostly on extracellular molecule production (Czaczyk and Myszka, 2007). The biosynthesis of EPS provides an optimal environment in which genetic material between the cells can be exchanged. This is needed for cell identification and the antigenic properties are helpful in serological characterization of the cells. Among the various compounds of extracellular carbohydrates are acetate esters, pyruvtes, formates, succinates, polysaccharides and proteins (Sutherland, 2001a).

The biofilm formation is usually assayed by using Congo Red Agar (CRA) plate test. According to a method developed by Freeman et al., (1989) the isolates are stored in nutrient agar slants and screened for biofilm formation ability using CRA plates. Biofilm forming strains are observed as dark black colonies while others as red colonies on the CRA plates. Recently, the concept of these biofims have changed with new imaging technologies, biochemical methods and molecular ecosystem biology tools. A biofilm structure can be observed in 3-D form to the nano-scale level (Neu and Lawrence, 2015). A lot of studies are being conducted on the physiology of the biofilm cells, the genotypic and phenotypic variation among the biofilm community, as well as the biofilm metabolome, proteome and transcriptome (Raes and Bork, 2008). This will help in the the development of efficient methods to control deleterious biofilms (clinical biofilms, food contaminants, biofouling on industrial equipment and on ship hulls) and to enhance and modulate beneficial ones

According to Li and Tian (2012) a pure-culture planktonic growth of bacteria is rarely found in natural environments.There is a physical interaction between the bacterial cells in biofilms (Kolenbrander, 2002; Watnick and Kolter,2000).The bacteria can organize into groups and can form well-organized communities. They also communicate for coordinated activities (Davey and O toole,2000; Watnick et al., 2000; Nadell et al., 2009). Quorum-sensing mechanisms are common in prokaryotic and single-celled eukaryotic organisms like fungi (van Bodman et al, 2008; Sordi and Muhlschlegal, 2009). For any biofilm structure to develop a high level of cell density is important (Kolenbrander et al., 2002; Kuramitsu et al., 2007 and Webb et al., 2003) and also for checking the effect of antibiotics against planktonic organisms in exponential growth phase using MIC and MBC.This can predict the antibiotic efficacy against rapidly dividing bacteria in acute infections. Papanna, Shobharani and Agrawal Renu (2010) studied the interception of quorum sensing signal molecule

Biofilms are resistant to antibiotics even at high concentrations (Costerton et al., 1999).This could happen when the diffusion of the antibiotic within the biofilm matrix is inefficient and results in slow growth rate of biofilm cells (Davey et al., 2000), there could be the presence of persistent cells and antibiotic-resistant small-colonies (Hogan and Kolter, 2002; Kolenbrander, 2000).Studies have proved that antibiotics can inhibit biofilm formation. An antibiotic azithromycin, is known to inhibit Pseudomonas aeruginosa biofilm. Biofilm colonies become resistant at higher concentrations of the antibiotics whereas at low concentrations these can be induced (Mah and OToole, 2001). P.aeruginosa is commonly present in the lungs of patients infested with cystic fibrosis. The clinical isolates show resistance to azithromycin (MIC>64 pg/ ml).However, low doses of azithromycin have shown improvement in lung function in patients with cystic fibrosis (Borriello et al., 2004). If antibiotics are given at low concentrations (below the MIC) than it induces biofilm formation in a variety of bacterial species. Sub-MIC concentrations of tobramycin can induce biofilm formation in P. aeruginosa. The use of antibiotics in agriculture, as growth promoters have shown to expose bacteria to low levels of the drugs and has caused havoc (Smith et al., 2002). Rachid et al. 

According to Fereshteh et al. (2020) microorganisms use biofilm to protect themselves against the harmful effects of the host body immune system and the surrounding environment. This helps them to survive against the anti-microbial agents. Inhibition of bacterial biofilm formation is very time consuming and expensive. Newer computational tools have been found to be a good option to predict the inhibition of biofilm peptides. In a computational prediction tool a large number of peptide sequences can be screened to select the peptides for validation. Vectors are extracted from the peptide primary structure and classification algorithms are carried out which includes SVM, random forest and k-nearest neighbour to evaluate their performance. Using a combination of features, helps in good evaluation. National Institute of Health (NIH) has found out that 80% of bacterial pathogens form biofilms and their multicellular structure makes them resistant to the hosts’ defense systems and traditional antimicrobials than planktonic bacteria. Recently, the use of Antimicrobial peptides

Joana et al.(2016) have written a critical review on biofilms and have discussed newer methods to study biofilms. These have given a deep knowledge on the physiology, structure and composition of biofilms. More polar amino acids were present in ABPs but QSPs were made up of higher number of neutral amino acids.This helps in recognition. Web application WebLogo help in generating sequence logos (Crooks et al., 2004). The uncharged polar amino acid is present at the first, third and fifth positions.The basis of SVM model is on the amino acid composition of the peptides. The Weka model is based on selected eight inputs which is trained on the NT5 dataset and is accurate, sensitive and specific.Peptide drugs are FDA approved and a total of 242 sequences of biotech peptides/proteins are available at the Drug Bank database. To identify potential anti-biofilm activity for characterization the peptide sequences are submitted on the module of dPABBs. The prediction outcomes are displayed under the ‘Putative ABPs’ section(http://ab-openlab.

Acinetobacter baumannii is an opportunistic pathogen giving rise to nosocomial infections causing threat to public health. Studies of biofilm-forming genes was done in A. baumannii isolates by PCR technique. To study the relationships of genes a technique based on PCR sequences along with multilocus sequence typing (MLST) were utilized (Saeed et al., 2020). Goudarzi, Mehdi et al. (2019) studied the genetic diversity and biofilm formation analysis of Staphylococcus aureus causing urinary tract infections in Tehran, Iran. The biofilm forming and adhesion encoding genes were studied along with distribution of different agr and spa types in S. aureus isolates by PCR screening and multiplex PCR. The workers found that the ability to produce biofilm was higher among MRSA strains as compared to MSSA strains. The most prevalent biofilm forming gene was icaD (77.3%), followed by icaA (76%), icaB (57.3%) and icaC (50.7%). Acinetobacter baumannii is a nosocomial pathogen which is commonly present in hospitals and is a causal organism of many diseases. A. baumannii isolates have been known as multidrug-resistant (MDR). For controlling such serious organism only molecular techniques have been found to be effective. 

Ali Demirci et al., (2014) studied the reactors with biofilms which are used to produce many value added products. These include organic acids, alcohols, enzymes, antibiotics, bacteriocins and many more. Many bioreactor designs favor the biofilm formation in a reactor. The biofilm reactors are utilized for fermentation and bioconversion of large amount of biomass. Recently, the biofilm reactors have been applied for production of many value-added products with novel designs. According to Ercan and Demirci (2015) the biofilms can cause both detrimental and beneficial effects in the environment. Biofilms in bioreactors has many advantages due to the membrane fouling which reduces the cost. Higher biomass density can be utilized and the operation is more stable.Biofilm reactors are commercially being utilized for waste water treatment, bench and pilot-scale production of value-added products. In order to run the biofilm reactor at optimum conditions it is important to understand the fundamentals of biofilm formation, the different properties

With recent work it has become clear that bacterial societies are very complex. Gene expression in bacterial communities are heterogenous. The heterogeneous gene expression contributes towards the biofilms in fluctuating environments which needs to be understood.Technique like single-cell analysis can help in the investigation of more complex communities. Recently, Jahid and Ha, (2012) have written a review on microbial biofilms of produce and the future challenges to food safety many outbreaks have been observed involving food- borne pathogens. Therefore, there is an urdent need for the safety of foods especially against microbial attacks and biofilm formation as they cause a risk to public health. Medically, the pathogenic microorganisms form biofilm- associated with the epithelial or endothelial lining which are embedded in the lungs, intestinal or vaginal mucus layer, the teeth or other medical implant surfaces or formed intracellularly (Dewasthale et al., 2018). Teichoic acids are characteristic major components of the cell surface in Gram-positive bacteria.

Abdallah M.2014. Biofilm formation and persistence on abiotic surfaces in the context of food and medical environments. Arch Microbiol. 196(7): 453-472. Abedon ST. 2011. Lysis from without. Bacteriophage. 1:46-49. Abu Bakar A, Ali M, Noor N M, Yahaya N, Ismail M and Abdullah A.2017. Bio-corrosion of carbon steel by sulfate reducing bacteria consortium in oil and gas pipelines. J Mech Eng Sci. 11: 2592-2600. Agnolucci M, Turrini A and Giovannetti M.2019.Molecular and functional characterization of beneficial bacteria associated with AMF spores. In:Methods in Rhizosphere Biology Research ed. Reinhardt D and Sharma AK.61-79. Singapore: Springer. Ahmad AL, Che Lah NF, Ismail S and Ooi BS.2012.Membrane antifouling methods and alternatives: ultrasound approach. Sep Purif Rev. 41: 318-346.