Effects of Stigeoclonium nanum, a freshwater periphytic microalga on water quality in a small-scale recirculating aquaculture system
Mohamed Ramli, Norulhuda ; Yusoff, Fatimah M. ; Giatsis, Christos ; Tan, Geok Yuan A. ; Verreth, Johan A.J. ; Verdegem, Marc C.J. - \ 2018
Aquaculture Research 49 (2018)11. - ISSN 1355-557X - p. 3529 - 3540.
ammonia - bacterial community - microalgae - nitrate - recirculating aquaculture system - Stigeoclonium nanum - water quality
Recirculating aquaculture systems (RAS) are becoming important for aquaculture due to land and water supply limitations and due to their low environmental impact. Bacteria are important in RAS as their role in nutrient recycling has been the main mechanism for waste removal in these systems. Besides bacteria, the presence of microalgae can benefit the water quality through the absorption of inorganic nitrogen (ammonium and nitrate) and phosphorus from the water. However, reports on the inclusion of microalgae in RAS are very scarce. The objective of this study was to determine the effect of microalgae on water quality (total ammonia nitrogen, nitrite, nitrate and phosphate) and bacterial composition in a freshwater small-scale RAS. A periphytic microalga, Stigeoclonium nanum, was used in this study. A rapid fingerprint analysis, denaturing gradient gel electrophoresis (DGGE), was used to determine the bacterial community composition in the water. The results showed that ammonia concentrations were not significantly different (p > 0.05) between RAS with microalgae (RAS+A) and RAS without microalgae (RAS-A). However, nitrite, nitrate and phosphate were significantly lower in the RAS+A than the RAS-A (p < 0.05). Pielou's evenness and Shannon diversity index of bacterial community between the treatments were not different (p > 0.05); however, the bacterial composition between the treatments was significantly different (p < 0.05).
Identifying the core microbial community in the gut of fungus-growing termites
Otani, S. ; Mikaelyan, A. ; Nobre, T. ; Hansen, L.H. ; Kone, N.A. ; Sorensen, S.J. ; Aanen, D.K. ; Boomsma, J.J. ; Brune, A. ; Poulsen, M. - \ 2014
Molecular Ecology 23 (2014)18. - ISSN 0962-1083 - p. 4631 - 4644.
feeding higher termite - bacterial community - phylogenetic analysis - functional-analysis - macrotermes-gilvus - lignin degradation - nasutitermes spp. - sp-nov. - diversity - hindgut
Gut microbes play a crucial role in decomposing lignocellulose to fuel termite societies, with protists in the lower termites and prokaryotes in the higher termites providing these services. However, a single basal subfamily of the higher termites, the Macrotermitinae, also domesticated a plant biomass-degrading fungus (Termitomyces), and how this symbiont acquisition has affected the fungus-growing termite gut microbiota has remained unclear. The objective of our study was to compare the intestinal bacterial communities of five genera (nine species) of fungus-growing termites to establish whether or not an ancestral core microbiota has been maintained and characterizes extant lineages. Using 454-pyrosequencing of the 16S rRNA gene, we show that gut communities have representatives of 26 bacterial phyla and are dominated by Firmicutes, Bacteroidetes, Spirochaetes, Proteobacteria and Synergistetes. A set of 42 genus-level taxa was present in all termite species and accounted for 56–68% of the species-specific reads. Gut communities of termites from the same genus were more similar than distantly related species, suggesting that phylogenetic ancestry matters, possibly in connection with specific termite genus-level ecological niches. Finally, we show that gut communities of fungus-growing termites are similar to cockroaches, both at the bacterial phylum level and in a comparison of the core Macrotermitinae taxa abundances with representative cockroach, lower termite and higher nonfungus-growing termites. These results suggest that the obligate association with Termitomyces has forced the bacterial gut communities of the fungus-growing termites towards a relatively uniform composition with higher similarity to their omnivorous relatives than to more closely related termites
Complementary symbiont contributions to plant decomposition in a fungus-farming termite
Poulsen, M. ; Hu, H. ; Li, C. ; Chen, Z. ; Xu, L. ; Otani, S. ; Nygaard, S. ; Nobre, T. ; Klaubauf, S. ; Schindler, P.M. ; Hauser, F. ; Pan, H. ; Yang, Z. ; Sonnenberg, A.S.M. ; Beer, W. de; Zhang, Y. ; Wingfield, M.J. ; Grimmelikhuijzen, C.J.P. ; Vries, R.P. de; Korb, J. ; Aanen, D.K. ; Wang, J. ; Boomsma, J.J. ; Zhang, G. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)40. - ISSN 0027-8424 - p. 14500 - 14505.
growing termites - bacterial community - gut microbiota - markov-models - genomes - termitomyces - evolution - tool - macrotermitinae - lignocellulose
Termites normally rely on gut symbionts to decompose organic matter but the Macrotermitinae domesticated Termitomyces fungi to produce their own food. This transition was accompanied by a shift in the composition of the gut microbiota, but the complementary roles of these bacteria in the symbiosis have remained enigmatic. We obtained high-quality annotated draft genomes of the termite Macrotermes natalensis, its Termitomyces symbiont, and gut metagenomes from workers, soldiers, and a queen. We show that members from 111 of the 128 known glycoside hydrolase families are represented in the symbiosis, that Termitomyces has the genomic capacity to handle complex carbohydrates, and that worker gut microbes primarily contribute enzymes for final digestion of oligosaccharides. This apparent division of labor is consistent with the Macrotermes gut microbes being most important during the second passage of comb material through the termite gut, after a first gut passage where the crude plant substrate is inoculated with Termitomyces asexual spores so that initial fungal growth and polysaccharide decomposition can proceed with high efficiency. Complex conversion of biomass in termite mounds thus appears to be mainly accomplished by complementary cooperation between a domesticated fungal monoculture and a specialized bacterial community. In sharp contrast, the gut microbiota of the queen had highly reduced plant decomposition potential, suggesting that mature reproductives digest fungal material provided by workers rather than plant substrate.
Ileal microbiota composition of broilers fed various commercial diet compositions
Hoeven-Hangoor, E. van der; Vossen, J.M.B.M. ; Schuren, F.H.J. ; Verstegen, M.W.A. ; Oliveira, J.E. de; Montijn, R.C. ; Hendriks, W.H. - \ 2013
Poultry Science 92 (2013)10. - ISSN 0032-5791 - p. 2713 - 2723.
gradient gel-electrophoresis - fatty-acids - gut microflora - xylanase supplementation - bacterial community - enterococcus-hirae - chickens - performance - ileum - feed
Microbiota plays a role in the release and absorption of nutrients from feed components, thereby affecting digesta composition and moisture content of the excreta. The objective of the current study was to determine the effects of 5 different diets varying in ingredients (medium-chain fatty acids, nonstarch polysaccharides, and starch) on the microbiota composition of ileal digesta of broiler chickens and excreta DM content. Each treatment was repeated 6 times in cages each containing 18 Ross 308 broilers, with growth performance measured from 0 to 34 d of age and excreta DM and ileal microbiota composition analyzed at 34 d of age. Microbiota composition was evaluated using a novel ribosomal RNA microarray technology containing 370 different probes covering various genera, groups of microbial species, and individual species of the chicken gut microbiota, of which 321 had a signal above the background threshold. Replacing part of the animal fat and soybean oil in the wheat-based diet with medium-chain fatty acids (MCFA; 0.3% C10 and 2.7% C12) improved feed efficiency compared with the other dietary treatments. This coincided with a suppression of gram-positive bacteria belonging to the phylum of the Firmicutes, including Lactobacillus species, and species belonging to the family of the Enterococcaceae and Micrococcaceae, whereas the gram-negative bacteria belonging to the family of the Enterobacteriaceae were promoted. None of the other diets used in the present study notably changed the ileal digesta bacteria composition. Excreta DM content was not affected by dietary treatment. The variation between individual birds per dietary treatment was more pronounced than variation caused by feed composition, with the exception of the digesta microbiota of the birds fed the MCFA diet. It is concluded that a diet with MCFA significantly changes the ileal microbiota composition, whereas the effect of the other diets on the composition of the microbiota and excreta DM content is small in broiler chickens.
Soil food web properties explain ecosystem services across European land use systems
Vries, F.T. de; Thebault, E.M.C. ; Liiri, M. ; Birkhofer, K. ; Tsiafouli, M. ; Bjornlund, L. ; Jorgensen, H.B. ; Brady, M.V. ; Christensen, S. ; Ruiter, P.C. de; Hertefeldt, T. d'; Frouz, J. ; Hedlund, K. ; Hemerik, L. ; Hol, W.H.G. ; Hotes, S. ; Mortimer, S.R. ; Setälä, H. ; Sgardelis, S.P. ; Uteseny, K. ; Putten, W.H. van der; Wolters, V. ; Bardgett, R.D. - \ 2013
Proceedings of the National Academy of Sciences of the United States of America 110 (2013)35. - ISSN 0027-8424 - p. 14296 - 14301.
nitrogen mineralization - carbon sequestration - bacterial community - mycorrhizal fungi - biomass - scale - intensification - decomposition - biodiversity - agriculture
Intensive land use reduces the diversity and abundance of many soil biota, with consequences for the processes that they govern and the ecosystem services that these processes underpin. Relationships between soil biota and ecosystem processes have mostly been found in laboratory experiments and rarely are found in the field. Here, we quantified, across four countries of contrasting climatic and soil conditions in Europe, how differences in soil food web composition resulting from land use systems (intensive wheat rotation, extensive rotation, and permanent grassland) influence the functioning of soils and the ecosystem services that they deliver. Intensive wheat rotation consistently reduced the biomass of all components of the soil food web across all countries. Soil food web properties strongly and consistently predicted processes of C and N cycling across land use systems and geographic locations, and they were a better predictor of these processes than land use. Processes of carbon loss increased with soil food web properties that correlated with soil C content, such as earthworm biomass and fungal/bacterial energy channel ratio, and were greatest in permanent grassland. In contrast, processes of N cycling were explained by soil food web properties independent of land use, such as arbuscular mycorrhizal fungi and bacterial channel biomass. Our quantification of the contribution of soil organisms to processes of C and N cycling across land use systems and geographic locations shows that soil biota need to be included in C and N cycling models and highlights the need to map and conserve soil biodiversity across the world.
Impact of long-term Diesel Contamination on Soil Microbial Community Structure
Sutton, N.B. ; Maphosa, F. ; Morillo, J.A. ; Abu Al-Soud, W. ; Langenhoff, A.A.M. ; Grotenhuis, J.T.C. ; Rijnaarts, H.H.M. ; Smidt, H. - \ 2013
Applied and Environmental Microbiology 79 (2013)2. - ISSN 0099-2240 - p. 619 - 630.
real-time pcr - bacterial community - hydrocarbon pollution - bioremediation - oil - diversity - biodegradation - degradation - microorganisms - gasoline
Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean samples showed higher diversity than contaminated samples (P <0.001). Bacterial phyla with high relative abundances in all samples included Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, and Chloroflexi. High relative abundances of Archaea, specifically of the phylum Euryarchaeota, were observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific operational taxonomic units (OTUs; defined using a 97% sequence identity threshold) in contaminated samples together suggest that natural attenuation of contamination has occurred. OTUs with sequence similarity to strictly anaerobic Anaerolineae within the Chloroflexi, as well as to Methanosaeta of the phylum Euryarchaeota, were detected. Anaerolineae and Methanosaeta are known to be associated with anaerobic degradation of oil-related compounds; therefore, their presence suggests that natural attenuation has occurred under anoxic conditions. This research underscores the usefulness of next-generation sequencing techniques both to understand the ecological impact of contamination and to identify potential molecular proxies for detection of natural attenuation.
The Influence of Long-Term Copper Contaminated Agricultural Soil at Different pH Levels on Microbial Communities and Springtail Transcriptional Regulation
Boer, T.E. de; Tas, N. ; Braster, M. ; Temminghoff, E.J.M. ; Roling, W.F.M. ; Roelofs, D. - \ 2012
Environmental Science and Technology 46 (2012)1. - ISSN 0013-936X - p. 60 - 68.
heavy-metal contamination - bacterial community - organic status - fungal communities - arable soil - sandy soil - diversity - toxicity - microorganisms - microarray
Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block. design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology.
Towards a renewed research agenda in ecotoxicology
Artigas, J. ; Arts, G.H.P. ; Babut, M. ; Caracciolo, A.B. ; Charles, S. ; Chaumot, A. ; Combourieu, B. ; Dahllöf, I. ; Despréaux, D. ; Ferrari, B. ; Friberg, N. ; Garric, J. ; Geffard, O. ; Gourlay-Francé, C. ; Hein, M. ; Hjorth, M. ; Krauss, M. ; Lange, H.J. de; Lahr, J. ; Lehtonen, K.K. ; Lettieri, T. ; Liess, M. ; Lofts, S. ; Mayer, P. ; Morin, S. ; Paschke, A. ; Svendsen, C. ; Usseglio-Polatera, P. ; Brink, N.W. van den; Vindimian, E. ; Williams, R. - \ 2012
Environmental Pollution 160 (2012). - ISSN 0269-7491 - p. 201 - 206.
effect-directed analysis - risk-assessment - intrinsic variability - invertebrate traits - bacterial community - multiple stressors - ecological traits - european rivers - toxicity tests - bioavailability
New concerns about biodiversity, ecosystem services and human health triggered several new regulations increasing the need for sound ecotoxicological risk assessment. The PEER network aims to share its view on the research issues that this challenges. PEER scientists call for an improved biologically relevant exposure assessment. They promote comprehensive effect assessment at several biological levels. Biological traits should be used for Environmental risk assessment (ERA) as promising tools to better understand relationships between structure and functioning of ecosystems. The use of modern high throughput methods could also enhance the amount of data for a better risk assessment. Improved models coping with multiple stressors or biological levels are necessary to answer for a more scientifically based risk assessment. Those methods must be embedded within life cycle analysis or economical models for efficient regulations. Joint research programmes involving humanities with ecological sciences should be developed for a sound risk management.
The therapeutic potential of manipulating gut microbiota in obesity and type 2 diabetes mellitus
Kootte, R.S. ; Vrieze, A. ; Holleman, F. ; Zoetendal, E.G. ; Vos, W.M. de; Groen, A.K. ; Hoekstra, J.B. ; Nieuwdorp, M. - \ 2012
Diabetes, Obesity & Metabolism 14 (2012)2. - ISSN 1462-8902 - p. 112 - 120.
diet-induced obesity - human intestinal microbiota - chain fatty-acids - lactobacillus-casei - bile-acids - in-vivo - gastrointestinal-tract - insulin-resistance - metagenomic analysis - bacterial community
Obesity and type 2 diabetes mellitus (T2DM) are attributed to a combination of genetic susceptibility and lifestyle factors. Their increasing prevalence necessitates further studies on modifiable causative factors and novel treatment options. The gut microbiota has emerged as an important contributor to the obesity-and T2DM-epidemic proposed to act by increasing energy harvest from the diet. Although obesity is associated with substantial changes in the composition and metabolic function of the gut microbiota, the pathophysiological processes remain only partly understood. In this review we will describe the development of the adult human microbiome and discuss how the composition of the gut microbiota changes in response to modulating factors. The influence of short-chain fatty acids, bile acids, prebiotics, probiotics, antibiotics and microbial transplantation is discussed from studies using animal and human models. Ultimately, we aim to translate these findings into therapeutic pathways for obesity and T2DM in humans
Daqu - a traditional Chinese liquor fermentation starter
Zheng, X. ; Rezaei Tabrizi, M. ; Nout, M.J.R. ; Han, B. - \ 2011
Journal of the Institute of Brewing 117 (2011)1. - ISSN 0046-9750 - p. 82 - 90.
luzhou-flavor liquor - bacterial community - microflora - strains - culture - zaopei - food
Chinese liquor is one of the world's oldest distilled alcoholic beverages, and it is typically obtained with the use of Daqufermentation starters. Daqu is a saccharifying and fermenting agent, having a significant impact on the flavour of the product. Daqucan be categorized according to maximum incubation temperatures (high, medium and low) and flavour (sauce, strong, light and miscellaneous). Most Daquare prepared by solid-state fermentation from wheat, barley and/or peas with ingredient formulation, grinding and mixing, shaping, incubation and maturation. Although there is a wealth of artisanal experience in the production of a range of different types of Daqu, the scientific knowledge base—including the microbiota, their enzymes and their metabolic activities—needs further development. Daquas a specific alcoholic starter is compared with other Asian amylolytic fermentation starters in terms of microbial diversity and function. Filamentous fungi (Rhizopus, Rhizomucor, Aspergillus and other genera), yeasts (Saccharomyces, Candida, Hansenula and other genera) and bacteria (acetic acid bacteria, lactic acid bacteria and Bacillus spp.), are considered to be the functional microbiota, responsible for the formation of a range of lytic enzymes, formation of substrates for alcoholic fermentation and formation of flavour compounds. However, the knowledge about the microbiota composition and their function is still fragmentary information, so further research is required to establish the functionality and growth kinetics of the microbiota in diverse types of Daqu.
Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples
Bogert, B. van den; Vos, W.M. de; Zoetendal, E.G. ; Kleerebezem, M. - \ 2011
Applied and Environmental Microbiology 77 (2011)6. - ISSN 0099-2240 - p. 2071 - 2080.
gastrointestinal-tract microbiota - ribosomal-rna genes - real-time pcr - phylogenetic microarray - quantitative-analysis - bacterial community - gut microbiome - fecal samples - extensive set - sequence data
Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results. An average of 7,944 pyrosequences, spanning the V1 and V2 region of 16S rRNA genes, was obtained per sample. Although primer choice in barcoded pyrosequencing did not affect species richness and diversity estimates, detection of Actinobacteria strongly depended on the selected primer. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis (HITChip) correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. Quantitative PCR was employed to investigate the deviations in profiling between pyrosequencing and HITChip analysis. Since cloning and sequencing of random 16S rRNA genes from ileostomy effluent confirmed the presence of novel intestinal phylotypes detected by pyrosequencing, especially those belonging to the Veillonella group, the divergence between pyrosequencing and the HITChip is likely due to the relatively low number of available 16S rRNA gene sequences of small intestinal origin in the DNA databases that were used for HITChip probe design. Overall, this study demonstrated that equivalent biological conclusions are obtained by high-throughput profiling of microbial communities, independent of technology or primer choice
Nematode succession during composting and the potential of the nematode community as an indicator of compost maturity
Steel, H. ; Peña, E. de la; Fonderie, P. ; Willekens, K. ; Borgonie, G. ; Bert, W. - \ 2010
Pedobiologia 53 (2010)3. - ISSN 0031-4056 - p. 181 - 190.
plant-parasitic nematodes - municipal solid-waste - bacterivorous nematodes - bacterial community - organic amendments - biological-control - enzyme-activities - faunal analysis - soil nematodes - food-web
One of the key issues in compost research is to assess when the compost has reached a mature stage. The maturity status of the compost determines the quality of the final soil amendment product. The nematode community occurring in a Controlled Microbial Composting (CMC) process was analyzed with the objective of assessing whether the species composition could be used as a bio-indicator of the compost maturity status. The results obtained here describe the major shifts in species composition that occur during the composting process. Compared to terrestrial ecosystems, nematode succession in compost differs mainly in the absence of K-strategists and numerical importance of diplogastrids. At the beginning of the composting process (thermophilic phase), immediately after the heat peak, the nematode population is primarily built by bacterial feeding enrichment opportunists (cp-1) (Rhabditidae, Panagrolaimidae, Diplogastridae) followed by the bacterial-feeding general opportunists (cp-2) (Cephalobidae) and the fungal-feeding general opportunists (Aphelenchoididae). Thereafter, during the cooling and maturation stage, the bacterial-feeding-predator opportunistic nematodes (Mononchoides sp.) became dominant. Finally, at the most mature stage, the fungal-feeding Anguinidae (mainly Ditylenchus filimus) were most present. Both, the Maturity Index (MI) and the fungivorous/bacterivorous ratio (f/b ratio), increase as the compost becomes more mature (ranging, respectively, from 1 to 1.86 and from 0 to 11.90). Based on these results, both indices are suggested as potential suitable tools to assess compost maturity
Soil biodiversity for agricultural sustainability
Brussaard, L. ; Ruiter, P.C. de; Brown, G.G. - \ 2007
Agriculture, Ecosystems and Environment 121 (2007)3. - ISSN 0167-8809 - p. 233 - 244.
ecosystem function relationship - microbial communities - functional stability - nitrogen mineralization - biological indicators - bacterial community - crusted soil - west-africa - diversity - productivity
We critically highlight some evidence for the importance of soil biodiversity to sustaining (agro-)ecosystem functioning and explore directions for future research. We first deal with resistance and resilience against abiotic disturbance and stress. There is evidence that soil biodiversity does confer stability to stress and disturbance, but the mechanism is not yet fully understood. It appears to depend on the kind of stress and disturbance and on the combination of stress and disturbance effects. Alternatively, community structure may play a role. Both possible explanations will guide further research. We then discuss biotic stress. There is evidence that soil microbial diversity confers protection against soil-borne disease, but crop and soil type and management also play a role. Their relative importance as well as the role of biodiversity in multitrophic interactions warrant further study. Henceforth, we focus on the effects of plant and soil biodiversity on nutrient and water use efficiencies as important ecological functions in agroecosystems. The available evidence suggests that mycorrhizal diversity positively contributes to nutrient and, possibly, water use efficiency. Soil fauna effects on nutrient and water use efficiencies are also apparent, but diversity effects may be indirect, through effects on soil structure. We present a conceptual diagram relating plant and soil biodiversity with soil structure and water and nutrient use efficiencies as a framework for future studies. We then consider how cropping systems design and management are interrelated and how management options might be interfaced with farmers¿ knowledge in taking management decisions. Finally, we attempt to express some economic benefits of soil biodiversity to society as part of a wider strategy of conserving and using agrobiodiversity.
The role of the commensal gut microbial community in broiler chickens
Lan, Y. ; Verstegen, M.W.A. ; Tamminga, S. ; Williams, B.A. ; Erdi, G. ; Boer, H. - \ 2005
Worlds Poultry Science Journal 61 (2005)1. - ISSN 0043-9339 - p. 95 - 104.
chain fatty-acids - competitive-exclusion - intestinal microflora - germ-free - conventional chicks - salmonella colonization - phylogenetic analysis - campylobacter-jejuni - bacterial community - cell proliferation
To understand the relationship between the gastrointestinal inhabiting microbial community and broiler health, a literature review is presented. The available information on the development of gut microbial community, the relationship between commensal microflora and digestive function, the role of gut microorganisms on competitive exclusion of chickens against pathogens, and modulation of the gut microbial community by addition of prebiotics to the diet is summarized. Gut dominant microbial communities become more complex as broilers grow older. The establishment of the dominant bacterial community is affected by dietary and host-related factors. Dietary prebiotics can modulate bacterial community shift towards non-harmful bacteria, which is beneficial for the health of broiler chickens. Gut commensal microorganisms play an important role in the prevention of colonization by pathogens in the gastrointestinal tract of chickens, a process known as competitive exclusion. In conclusion, the dilemma caused by the forthcoming ban of antibiotics feed additives and need to maintain the intestinal health of broiler chickens, has produced an enormous interest in finding alternatives. Modulating the intestinal microbial community in a healthy direction, by dietary ingredients such as prebiotics, could be a good solution.