Environmental Microbiology
Water Microbiology
The new book on Environmental Microbiology: Current Technology and Water Applications edited by Keya Sen and Nicholas J. Ashbolt has been delivered to our distributors and is available for immediate dispatch read more ...
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 | Edited by: Keya Sen and Nicholas J. Ashbolt ISBN: 978-1-904455-70-7 Publisher: Caister Academic Press Publication Date: January 2011 Cover: hardback |
Ecology of Baculoviruses
from Jenny S. Cory in Insect Virology
Ecological studies involving insect viruses have centred on baculoviruses, partly because they are associated with population declines of some insect species, and also because they are highly pathogenic to insects, making them ideal candidates for pest control. Recent research has focussed on four main areas; (i) the influence of host condition on resistance to viral infection, (ii) the role and maintenance of baculovirus diversity, (iii) the prevalence of covert infections, and (iv) the elucidation of patterns of host resistance in field populations.
Tritrophic interactions, either via direct effects of plant secondary chemicals or through nutritionally mediated changes in host immunity, can have a significant impact on baculovirus efficacy. Variation within baculovirus populations appears to be ubiquitous, and mixed genotype infections apparently act to generate higher levels of pathogenicity. Covert infections are increasingly being shown to be common in field populations of Lepidoptera but their importance in generating overt baculovirus infections is still unclear. Field studies on forest insects indicate that host resistance varies with fluctuating host density and condition. Synthesis of the impacts of host condition on susceptibility, the role of genetic variability in infection, and of the relationship between overt and covert infection, will promote understanding of the ecological interactions between baculoviruses and natural host populations.
Further reading: Insect Virology
Ecological studies involving insect viruses have centred on baculoviruses, partly because they are associated with population declines of some insect species, and also because they are highly pathogenic to insects, making them ideal candidates for pest control. Recent research has focussed on four main areas; (i) the influence of host condition on resistance to viral infection, (ii) the role and maintenance of baculovirus diversity, (iii) the prevalence of covert infections, and (iv) the elucidation of patterns of host resistance in field populations.
Tritrophic interactions, either via direct effects of plant secondary chemicals or through nutritionally mediated changes in host immunity, can have a significant impact on baculovirus efficacy. Variation within baculovirus populations appears to be ubiquitous, and mixed genotype infections apparently act to generate higher levels of pathogenicity. Covert infections are increasingly being shown to be common in field populations of Lepidoptera but their importance in generating overt baculovirus infections is still unclear. Field studies on forest insects indicate that host resistance varies with fluctuating host density and condition. Synthesis of the impacts of host condition on susceptibility, the role of genetic variability in infection, and of the relationship between overt and covert infection, will promote understanding of the ecological interactions between baculoviruses and natural host populations.
Further reading: Insect Virology
Sensory Mechanisms in Bacteria
from Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition
Bacteria have evolved extraordinary abilities to detect physical and chemical signals, both within their own cells and in the extracellular environment. The interaction of a signal with its receptor (usually a protein or RNA molecule) triggers a series of events that lead to reprogramming of cellular physiology, typically as a consequence of altered patterns of gene expression. In this way, the bacterial cell is able to mount appropriate and effective responses to changing physical and/or chemical environments. The versatility with which many bacteria adapt to environmental change underlies many important aspects of microbiology. For example, pathogens encounter multiple environments as they invade a host from the outside, and then progress through different sites within host tissues. There is growing evidence that pathogenic bacteria make use of physical and chemical cues to signal their presence in a suitable host, and need to adapt to the host environment in order to mount a successful infection. On the other hand, it should not be assumed that all signals to which bacteria must respond originate in the extracellular environment. For many species, even the cosseted life in a laboratory shake flask is 'stressful', in the sense that there is often a need to avoid or reverse the effects of harmful intermediates or by-products of metabolism. For example, all organisms that use dioxygen as a terminal electron acceptor have to deal with the reactive oxygen species that arise as adventitious by-products of aerobic metabolism. In bacteria, multiple protein receptors for oxygen radicals have been described, which control the expression of genes encoding enzymes that detoxify oxygen radicals or repair the damage that they cause.
Further reading: Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition
Bacteria have evolved extraordinary abilities to detect physical and chemical signals, both within their own cells and in the extracellular environment. The interaction of a signal with its receptor (usually a protein or RNA molecule) triggers a series of events that lead to reprogramming of cellular physiology, typically as a consequence of altered patterns of gene expression. In this way, the bacterial cell is able to mount appropriate and effective responses to changing physical and/or chemical environments. The versatility with which many bacteria adapt to environmental change underlies many important aspects of microbiology. For example, pathogens encounter multiple environments as they invade a host from the outside, and then progress through different sites within host tissues. There is growing evidence that pathogenic bacteria make use of physical and chemical cues to signal their presence in a suitable host, and need to adapt to the host environment in order to mount a successful infection. On the other hand, it should not be assumed that all signals to which bacteria must respond originate in the extracellular environment. For many species, even the cosseted life in a laboratory shake flask is 'stressful', in the sense that there is often a need to avoid or reverse the effects of harmful intermediates or by-products of metabolism. For example, all organisms that use dioxygen as a terminal electron acceptor have to deal with the reactive oxygen species that arise as adventitious by-products of aerobic metabolism. In bacteria, multiple protein receptors for oxygen radicals have been described, which control the expression of genes encoding enzymes that detoxify oxygen radicals or repair the damage that they cause.
Further reading: Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition
Detection of Viable Organisms Using Molecular Techniques
from Paul A. Rochelle, Anne K. Camper, Andreas Nocker and Mark Burr in Environmental Microbiology: Current Technology and Water Applications
The ultimate measure of microbial viability and biological activity is growth in some form of culture system. Unfortunately, due to many limitations, growth is usually not the most sensitive or rapid detection method. Many molecular-based tools are available for assessing viability and functional gene expression, and have applications for specific microbes in environmental samples. Methods include fluorescent nucleic acid binding dyes, enzymatic conversion of substrates to fluorescent compounds (often in conjunction with nucleic acid-based methods), various techniques based on amplification and detection of nucleic acids, nucleic acid amplification linked to biosensors and microarray detection platforms, detection and characterization of proteins, and molecular detection coupled with culturing.
Further reading:
The ultimate measure of microbial viability and biological activity is growth in some form of culture system. Unfortunately, due to many limitations, growth is usually not the most sensitive or rapid detection method. Many molecular-based tools are available for assessing viability and functional gene expression, and have applications for specific microbes in environmental samples. Methods include fluorescent nucleic acid binding dyes, enzymatic conversion of substrates to fluorescent compounds (often in conjunction with nucleic acid-based methods), various techniques based on amplification and detection of nucleic acids, nucleic acid amplification linked to biosensors and microarray detection platforms, detection and characterization of proteins, and molecular detection coupled with culturing.
Further reading:
Identity of Single Microbial Cells
from Daniel S. Read and Andrew S. Whiteley in Environmental Microbiology: Current Technology and Water Applications
Linking both identity and function within microbial communities has long been seen as essential for understanding the role that bacteria play in the environment. Techniques based on the study of single microbial cells offer a unique approach that provides information about heterogeneity within populations, and the role of spatial organization within the environment. Various single-cell techniques are currently in use for the study of microbial ecology, an important one being Raman spectroscopy. This technique can be used for studying different features of microbial systems. Raman spectroscopy can be used in combination with Fluorescence in situ Hybridization (FISH) and Stable Isotope Probing (SIP), which together can be utilized to gain an insight into the identity and function of single bacterial cells in situ.
Further reading:
Linking both identity and function within microbial communities has long been seen as essential for understanding the role that bacteria play in the environment. Techniques based on the study of single microbial cells offer a unique approach that provides information about heterogeneity within populations, and the role of spatial organization within the environment. Various single-cell techniques are currently in use for the study of microbial ecology, an important one being Raman spectroscopy. This technique can be used for studying different features of microbial systems. Raman spectroscopy can be used in combination with Fluorescence in situ Hybridization (FISH) and Stable Isotope Probing (SIP), which together can be utilized to gain an insight into the identity and function of single bacterial cells in situ.
Further reading:
Amoebae as a Tool
from Julia Lienard and Gilbert Greub in Environmental Microbiology: Current Technology and Water Applications
Obligate intracellular microorganisms are unculturable by classic axenic culture methods. As a result they have largely been overlooked, despite many being significant human and animal pathogens. Resistance of amoeba-resisting microorganisms (ARM) to amoebal destruction may predict ability to also resist mammalian macrophages, which are somehow similar to amoebae and represent one of the first cellular immune defenses in mammals. Thus, general approaches have been described for the growth of strict intracellular microorganisms, using amoebae as hosts in a cell culture system. Such an approach has been shown to be advantageous, since amoebal co-culture will selectively grow microorganisms that resist these professional phagocytes. An alternative approach for the isolation of novel ARM is also available, which requires the isolation of new amoebal strains by amoebal enrichment on a suitable prey (such as Escherichia coli), and then to search for intra-amoebal microorganisms within the isolated amoebae. Once new potentially pathogenic ARM has been isolated, one should then further assess the potential infectivity of these intracellular microorganisms. The application of macrophages, as an in vitro model to test microbial virulence is also possible.
Further reading:
Obligate intracellular microorganisms are unculturable by classic axenic culture methods. As a result they have largely been overlooked, despite many being significant human and animal pathogens. Resistance of amoeba-resisting microorganisms (ARM) to amoebal destruction may predict ability to also resist mammalian macrophages, which are somehow similar to amoebae and represent one of the first cellular immune defenses in mammals. Thus, general approaches have been described for the growth of strict intracellular microorganisms, using amoebae as hosts in a cell culture system. Such an approach has been shown to be advantageous, since amoebal co-culture will selectively grow microorganisms that resist these professional phagocytes. An alternative approach for the isolation of novel ARM is also available, which requires the isolation of new amoebal strains by amoebal enrichment on a suitable prey (such as Escherichia coli), and then to search for intra-amoebal microorganisms within the isolated amoebae. Once new potentially pathogenic ARM has been isolated, one should then further assess the potential infectivity of these intracellular microorganisms. The application of macrophages, as an in vitro model to test microbial virulence is also possible.
Further reading:
Detection of Pathogens in Water Using Microarrays
from Timothy M. Straub in Environmental Microbiology: Current Technology and Water Applications
For waterborne pathogen monitoring, regulatory agencies have traditionally focused on developing a single method for an existing or emerging pathogen in water supplies. However, the ability to use a single method to determine all potential pathogens or indicators in a water supply would be particularly advantageous. Such an approach has three major hurdles: 1) sensitive detection of highly dilute pathogens in a water supply, 2) specific detection of pathogens from non-pathogenic near-neighbors, and 3) multiplexed strategies that preserve the sensitivity and specificity of the assay.
Further reading:
For waterborne pathogen monitoring, regulatory agencies have traditionally focused on developing a single method for an existing or emerging pathogen in water supplies. However, the ability to use a single method to determine all potential pathogens or indicators in a water supply would be particularly advantageous. Such an approach has three major hurdles: 1) sensitive detection of highly dilute pathogens in a water supply, 2) specific detection of pathogens from non-pathogenic near-neighbors, and 3) multiplexed strategies that preserve the sensitivity and specificity of the assay.
Further reading:
Low Cost Screening of Multiple Waterborne Pathogens
from Seyrig et al in Environmental Microbiology: Current Technology and Water Applications
A vast array of low cost, simple, rugged, and rapid molecular approaches are emerging for the detection of indicators and pathogens, along with the collection of relevant genotypic information. Loop-mediated isothermal amplification (LAMP) is a relatively new DNA amplification technique, which due to its simplicity, ruggedness, and low cost could provide major advantages to the water industry. In LAMP, the target sequence is amplified at a constant temperature using either two or three sets of primers and a polymerase with high strand displacement activity. Due to the specific nature of the action of these primers, the amount of DNA produced in LAMP is considerably higher than PCR based amplification. The corresponding release of pyrophosphate results in visible turbidity due to precipitation, which allows easy visualization by the naked eye, especially for larger reaction volumes or via simple detection approaches for smaller volumes. The reaction can be followed in real-time either by measuring the turbidity or the signals from DNA produced via fluorescent dyes that intercalate or directly label the DNA, and in turn can be correlated to the number of copies initially present. Hence, LAMP can also be quantitative. While LAMP is already the method of choice in organizations engaged in combating infectious diseases such as tuberculosis, malaria, and sleeping sickness in developing regions, it has yet to be extensively validated for commonly known waterborne pathogens.
Further reading:
A vast array of low cost, simple, rugged, and rapid molecular approaches are emerging for the detection of indicators and pathogens, along with the collection of relevant genotypic information. Loop-mediated isothermal amplification (LAMP) is a relatively new DNA amplification technique, which due to its simplicity, ruggedness, and low cost could provide major advantages to the water industry. In LAMP, the target sequence is amplified at a constant temperature using either two or three sets of primers and a polymerase with high strand displacement activity. Due to the specific nature of the action of these primers, the amount of DNA produced in LAMP is considerably higher than PCR based amplification. The corresponding release of pyrophosphate results in visible turbidity due to precipitation, which allows easy visualization by the naked eye, especially for larger reaction volumes or via simple detection approaches for smaller volumes. The reaction can be followed in real-time either by measuring the turbidity or the signals from DNA produced via fluorescent dyes that intercalate or directly label the DNA, and in turn can be correlated to the number of copies initially present. Hence, LAMP can also be quantitative. While LAMP is already the method of choice in organizations engaged in combating infectious diseases such as tuberculosis, malaria, and sleeping sickness in developing regions, it has yet to be extensively validated for commonly known waterborne pathogens.
Further reading:
- Environmental Microbiology: Current Technology and Water Applications
- Nanotechnology in Water Treatment Applications
- Metagenomics: Theory, Methods and Applications
- Environmental Molecular Microbiology
Biosensors for the Detection of Waterborne Pathogens
from Sen Xu and Raj Mutharasan in Environmental Microbiology: Current Technology and Water Applications
The detection of waterborne pathogens and toxins by biosensor-based methods are becoming increasingly important. Optical, electrochemical and electromechanical sensors are available and surface chemistries are being used for immobilizing biorecognition molecules on sensor surfaces. Topics that are important include representative sensor responses, limit of detections (LOD) and time to results (TTR).
Further reading:
The detection of waterborne pathogens and toxins by biosensor-based methods are becoming increasingly important. Optical, electrochemical and electromechanical sensors are available and surface chemistries are being used for immobilizing biorecognition molecules on sensor surfaces. Topics that are important include representative sensor responses, limit of detections (LOD) and time to results (TTR).
Further reading:
Detection of Microbes in Water
from Keya Sen in Environmental Microbiology: Current Technology and Water Applications
Molecular techniques based on genomics, proteomics and transcriptomics are rapidly growing as complete microbial genome sequences are becoming available, and advances are made in sequencing technology, analytical biochemistry, microfluidics and data analysis. While the clinical and food industries are increasingly adapting these techniques, there appear to be major challenges in detecting health-related microbes in source and treated drinking waters. This is due in part to the low density of pathogens in water, necessitating significant processing of large volume samples. From the vast panorama of available molecular techniques, some are finding a place in the water industry: Quantitative PCR, protein detection and immunological approaches, loop-mediated isothermal amplification (LAMP), microarrays.
Further reading:
Molecular techniques based on genomics, proteomics and transcriptomics are rapidly growing as complete microbial genome sequences are becoming available, and advances are made in sequencing technology, analytical biochemistry, microfluidics and data analysis. While the clinical and food industries are increasingly adapting these techniques, there appear to be major challenges in detecting health-related microbes in source and treated drinking waters. This is due in part to the low density of pathogens in water, necessitating significant processing of large volume samples. From the vast panorama of available molecular techniques, some are finding a place in the water industry: Quantitative PCR, protein detection and immunological approaches, loop-mediated isothermal amplification (LAMP), microarrays.
Further reading:
Biofilms
from "Nanozymes for Biofilm Removal" Melanie Richards and Thomas Eugene Cloete in Nanotechnology in Water Treatment Applications
Sessile communities of bacteria encased in extracellular polymeric substances (EPS) are known as biofilms and causes serious problems in various areas, amongst other, the medical industry, industrial water settings, paper industry and food processing industry. Although various methods of biofilm control exist, these methods are not without limitations and often fail to remove biofilms from surfaces. Biofilms often show reduced susceptibility to antimicrobials or chemicals and chemical by-products may be toxic to the environment, whereas mechanical methods may be labour intensive and expensive due to down-time required to clean the system.
Further reading:
Sessile communities of bacteria encased in extracellular polymeric substances (EPS) are known as biofilms and causes serious problems in various areas, amongst other, the medical industry, industrial water settings, paper industry and food processing industry. Although various methods of biofilm control exist, these methods are not without limitations and often fail to remove biofilms from surfaces. Biofilms often show reduced susceptibility to antimicrobials or chemicals and chemical by-products may be toxic to the environment, whereas mechanical methods may be labour intensive and expensive due to down-time required to clean the system.
Further reading:
Risk assessment of nanoparticles and nanomaterials
from Michele de Kwaadsteniet and Thomas Eugene Cloete in Nanotechnology in Water Treatment Applications
The risk assessment of nanoparticles and nanomaterials is of key importance for the continous development in the already striving new field of nanotechnology. Humans are increasingly being exposed to nanoparticles and nanomaterials, placing stress on the development and validation of reproducible toxicity tests. Tests currently used include genotoxicity and cytotoxicity tests, and in vivo toxicity models. The unique characteristics of nanoparticles and nanomaterials are responsible for their toxicity and interaction with biological macromolecules within the human body. This may lead to the development of diseases and clinical disorders. A loss in cell viability and structure can also occur in exposed tissues as well as inflammation and granuloma formation. The future of nanotechnology depends on the responsible assessment of nanoparticles and nanomaterials.
Further reading: Nanotechnology in Water Treatment Applications
The risk assessment of nanoparticles and nanomaterials is of key importance for the continous development in the already striving new field of nanotechnology. Humans are increasingly being exposed to nanoparticles and nanomaterials, placing stress on the development and validation of reproducible toxicity tests. Tests currently used include genotoxicity and cytotoxicity tests, and in vivo toxicity models. The unique characteristics of nanoparticles and nanomaterials are responsible for their toxicity and interaction with biological macromolecules within the human body. This may lead to the development of diseases and clinical disorders. A loss in cell viability and structure can also occur in exposed tissues as well as inflammation and granuloma formation. The future of nanotechnology depends on the responsible assessment of nanoparticles and nanomaterials.
Further reading: Nanotechnology in Water Treatment Applications
Nanotechnology and Water Microbiology
Nanotechnology is the engineering and art of manipulating matter at the nanoscale (1-100 nm) level. Nanotechnology offers the potential of novel nanomaterials for the treatment of surface water, groundwater and wastewater contaminated by toxic metal ions, organic and inorganic solutes and microorganisms. At the present time many nanomaterials are under active research and development.
Further reading: Nanotechnology in Water Treatment Applications
Further reading: Nanotechnology in Water Treatment Applications
Biofilm Removal using Nanozymes
from Melanie Richards and Thomas Eugene Cloete in Nanotechnology in Water Treatment Applications
Recently there has been a great interest in the enzymatic degradation of biofilms. Enzymes are highly selective and disrupt the structural stability of the biofilm EPS matrix. Various studies have focused on the enzymatic degradation of polysaccharides and proteins for biofilm detachment since these are the two dominant components of the EPS. Due to the structural role of proteins and polysaccharides in the EPS matrix, a combination of various proteases and polysaccharases may be successful in biofilm removal.
The biodegradability and low toxicity of enzymes also make them attractive biofilm control agents. Regardless of all the advantages associated with enzymes, they also suffer from various drawbacks given that they are relatively expensive, show insufficient stability or activity under certain conditions, and cannot be reused. Various approaches are being used to increase the stability of enzymes, including enzyme modification, enzyme immobilization, protein engineering and medium engineering. Although these conventional methods have been used frequently to improve the stability of enzymes, various new techniques, such as self-immobilization of enzymes, the immobilization of enzymes on nano-scale structures and the production of single-enzyme nanoparticles, have been developed.
Self-immobilization of enzymes entails the cross-linking of enzyme molecules with each other and yields final preparations consisting of essentially pure proteins and high concentrations of enzyme per unit volume. The activity, stability and efficiency of immobilized enzymes can be improved by reducing the size of the enzyme-carrier. Nano-scale carrier materials allow for high enzyme loading per unit mass, catalytic recycling and a reduced loss of enzyme activity. Furthermore, enzymes can be stabilized by producing single-enzyme nanoparticles consisting of single-enzyme molecules surrounded by a porous organic-inorganic network of less than a few nanometers thick.
All these new technologies of enzyme stabilization make enzymes even more attractive alternatives to other biofilm removal and control agents.
Further reading:
Recently there has been a great interest in the enzymatic degradation of biofilms. Enzymes are highly selective and disrupt the structural stability of the biofilm EPS matrix. Various studies have focused on the enzymatic degradation of polysaccharides and proteins for biofilm detachment since these are the two dominant components of the EPS. Due to the structural role of proteins and polysaccharides in the EPS matrix, a combination of various proteases and polysaccharases may be successful in biofilm removal.
The biodegradability and low toxicity of enzymes also make them attractive biofilm control agents. Regardless of all the advantages associated with enzymes, they also suffer from various drawbacks given that they are relatively expensive, show insufficient stability or activity under certain conditions, and cannot be reused. Various approaches are being used to increase the stability of enzymes, including enzyme modification, enzyme immobilization, protein engineering and medium engineering. Although these conventional methods have been used frequently to improve the stability of enzymes, various new techniques, such as self-immobilization of enzymes, the immobilization of enzymes on nano-scale structures and the production of single-enzyme nanoparticles, have been developed.
Self-immobilization of enzymes entails the cross-linking of enzyme molecules with each other and yields final preparations consisting of essentially pure proteins and high concentrations of enzyme per unit volume. The activity, stability and efficiency of immobilized enzymes can be improved by reducing the size of the enzyme-carrier. Nano-scale carrier materials allow for high enzyme loading per unit mass, catalytic recycling and a reduced loss of enzyme activity. Furthermore, enzymes can be stabilized by producing single-enzyme nanoparticles consisting of single-enzyme molecules surrounded by a porous organic-inorganic network of less than a few nanometers thick.
All these new technologies of enzyme stabilization make enzymes even more attractive alternatives to other biofilm removal and control agents.
Further reading:
Metagenomics book review
The following excerpt is from a recent book review of Metagenomics: Theory, Methods and Applications:
"an excellent resource for students, researchers, and scientists ... a valuable resource on the newly evolving biological field of metagenomics, making contributions to ecology, biodiversity, bioremediation, bioprospection of natural products, medicine, and other disciplines." from Omer Iqbal (Loyola University Medical Center) writing in Doodys read more ...
"an excellent resource for students, researchers, and scientists ... a valuable resource on the newly evolving biological field of metagenomics, making contributions to ecology, biodiversity, bioremediation, bioprospection of natural products, medicine, and other disciplines." from Omer Iqbal (Loyola University Medical Center) writing in Doodys read more ...
 | Edited by: Diana Marco ISBN: 978-1-904455-54-7 Publisher: Caister Academic Press Publication Date: January 2010 Cover: Hardback read more ... |
Conference Update: Harnessing The Power of Microbes
October 4 - 7, 2010 Harnessing The Power of Microbes for Better Food, Agro-industry, Health and Environment
Bogor, Indonesia Further information
International Seminar of the Indonesian Society for Microbiology. The seminar aims to provide a platform for international microbiologists, biotechnologists, policy makers and the private sector to interact and exchange the latest ideas and techniques in microbiology and biotechnologySuggested reading: Environmental Molecular Microbiology
Bogor, Indonesia Further information
International Seminar of the Indonesian Society for Microbiology. The seminar aims to provide a platform for international microbiologists, biotechnologists, policy makers and the private sector to interact and exchange the latest ideas and techniques in microbiology and biotechnologySuggested reading: Environmental Molecular Microbiology
Conference Update: Food Microbiology
August 30 - September 3, 2010 22nd International ICFMH Symposium, Food Micro 2010
Copenhagen, Denmark Further information
Special emphasis will be on how microbes respond to changes in their environment and the congress will address applied and fundamental aspects of microbial behaviour in: Food fermentation and spoilage, Adverse environments, Risk assessment, Food production, The intestinal tract
Suggested reading: Environmental Microbiology Books
Copenhagen, Denmark Further information
Special emphasis will be on how microbes respond to changes in their environment and the congress will address applied and fundamental aspects of microbial behaviour in: Food fermentation and spoilage, Adverse environments, Risk assessment, Food production, The intestinal tract
Suggested reading: Environmental Microbiology Books