Use of pyrosequencing and denaturing gradient gel electrophoresis to examine the effects of probiotics and essential oil blends on digestive microflora in broilers under mixed Eimeria infection

Orally delivered Bacillus subtilis expressing chicken NK-2 peptide stabilizes gut microbiota and enhances intestinal health and local immunity in coccidiosis-infected broiler chickens

We recently reported a stable Bacillus subtilis-carrying chicken NK-lysin peptide (B. subtilis-cNK-2) as an effective oral delivery system of an antimicrobial peptide to the gut with therapeutic effect against Eimeria parasites in broiler chickens. To further investigate the effects of a higher dose of an oral B. subtilis-cNK-2 treatment on coccidiosis, intestinal health, and gut microbiota composition, 100 (14-day-old) broiler chickens were allocated into 4 treatment groups in a randomized design: 1) uninfected control (CON), 2) infected control without B. subtilis (NC), 3) B. subtilis with empty vector (EV), and 4) B. subtilis with cNK-2 (NK). All chickens, except the CON group, were infected with 5,000 sporulated Eimeria acervulina (E. acervulina) oocysts on d 15. Chickens given B. subtilis (EV and NK) were orally gavaged (1 × 10¹² cfu/mL) daily from d 14 to 18. Growth performances were measured on d 6, 9, and 13 postinfection (dpi). Spleen and duodenal samples were collected on 6 dpi to assess the gut microbiota, and gene expressions of gut integrity and local inflammation makers. Fecal samples were collected from 6 to 9 dpi to enumerate oocyst shedding. Blood samples were collected on 13 dpi to measure the serum 3-1E antibody levels. Chickens in the NK group showed significantly improved (P < 0.05) growth performance, gut integrity, reduced fecal oocyst shedding and mucosal immunity compared to NC. Interestingly, there was a distinct shift in the gut microbiota profile in the NK group compared to that of NC and EV chickens. Upon challenge with E. acervulina, the percentage of Firmicutes was reduced and that of Cyanobacteria increased. In NK chickens, however, the ratio between Firmicutes and Cyanobacteria was not affected and was similar to that of CON chickens. Taken together, NK treatment restored dysbiosis incurred by E. acervulina infection and showed the general protective effects of orally delivered B. subtilis-cNK-2 on coccidiosis infection. This includes reduction of fecal oocyst shedding, enhancement of local protective immunity, and maintenance of gut microbiota homeostasis in broiler chickens.

Effect of blending encapsulated essential oils and organic acids as an antibiotic growth promoter alternative on growth performance and intestinal health in broilers with necrotic enteritis

The effects of a blend of encapsulated organic acids with essential oils (EOA) as an alternative to antimicrobial growth promoter (AGP) on growth performance and gut health of Eimeria spp./Clostridium perfringens (C. perfringens) in chickens infected with necrotic enteritis (NE) broilers was investigated. A total of 432 male Arbor Acres broilers (1-day-old) were randomly distributed into 6 treatment groups, namely noninfected negative control (A); NE-infected positive control (D); NE-infected broiler chickens fed a basal diet supplemented with 250 mg/kg bacitracin methylene disalicylate (BMD) plus 90 mg/kg monensin; and NE-infected broiler chicken fed 200; 500; and 800 mg/kg EOA (E, F, G, and H group). Feeding EOA at 200 and 500 mg/kg considerably improved the feed conversion ratio, reduced gut lesions, serum fluorescein isothiocyanate dextran level, and C. perfringens load in the caecum and liver of the NE-infected broiler chickens. This feed was similar to AGP. Furthermore, the increased villous height-to-crypt depth ratio and goblet cells counts, upregulated claudin-1, glucagon-like peptide-2 (GLP-2), insulin-like growth factor-2 (IGF-2) mRNA gene expression, downregulated occludin, zonula occludens-1 (ZO-1), toll-like receptor (TLR-4), interleukin (IL-1β), interferon γ (IFN-γ), TNF receptor-associated factor 6 (TRAF-6), tumor necrosis factor superfamily member 15 (TNFSF15), and Toll-interacting protein (Tollip) genes expression in the jejunum were observed in the NE-infected broiler chickens that received EOA at 200 and 500 mg/kg compared with those of the single NE-challenged groups without EOA supplementations (P < 0.05). The 16S analysis revealed that EOA supplemented with 200 or 500 mg/kg enriched relative abundance of Lactobacillus, unclassified_Lachnospiraceae, and Enterococcus, and carbohydrate metabolic pathways but suppressed unclassified_Erysipelotrichacease and organismal systems involved in the immune system (P < 0.05). Feeding EOA could alleviate NE-induced gut impairment and growth depression and modulate cecal microbiota composition, which has potential as antimicrobial alternatives.

Effects of Different Ambient Temperatures on Caecal Microbial Composition in Broilers

Short-term or acute temperature stress affect the immune responses and alters the gut microbiota of broilers, but the influences of long-term temperature stress on stress biomarkers and the intestinal microbiota remains largely unknown. Therefore, we examined the effect of three long-term ambient temperatures (high (HC), medium (MC), and low (LC) temperature groups) on the gene expression of broilers’ heat shock proteins (Hsps) and inflammation – related genes, as well as the caecal microbial composition. The results revealed that Hsp70 and Hsp90 levels in HC group significantly increased, and levels of Hsp70, Hsp90, IL-6, TNF-α, and NFKB1 in LC group were significantly higher than in MC group (p < 0.05). In comparison with the MC group, the proportion of Firmicutes increased in HC and LC groups, while that of Bacteroidetes decreased in LC group at phylum level (p < 0.05). At genus level, the proportion of Escherichia/Shigella, Phascolarctobacterium, Parabacteroides,and Enterococcus increased in HC group; the fraction of Faecalibacterium was higher in LC group; and the percentage of Barnesiella and Alistipes decreased in both HC and LC groups (p < 0.05). Functional analysis based on communities’ phylogenetic investigation revealed that the pathways involved in environmental information processing and metabolism were enriched in the HC group. Those involved in cellular processes and signaling, metabolism, and gene regulation were enriched in LC group. Hence, we conclude that the long-term temperature stress can greatly alter the intestinal microbial communities in broilers and may further affect the host’s immunity and health.

Effects of Colombian oregano essential oil (Lippia origanoides Kunth) and Eimeria species on broiler production and cecal microbiota

The gut microbiota has an important effect on poultry health and production. The aim of this study was to evaluate the effect of Colombian oregano (COO), Lippia origanoides Kunth, essential oil supplementation on broiler chicken performance and their cecal bacterial microbiome by 16S-based sequencing. Essential oil was extracted by steam distillation and analyzed by Gas chromatography/mass spectrometry. Two COO levels in feed, 0 ppm control (C) and 100 ppm (O), were evaluated in 2 groups of broilers either unchallenged (U) or challenged (E) with a viable attenuated Eimeria (coccidia) oocyte vaccine. Four treatments, UC, UO, EC, and EO, were distributed among 720 one-day-old male Ross broilers randomly placed in 24 pens. Cecal contents DNA was extracted and pyrosequencing was performed following a standard procedure. Pyrosequencing data were processed, and sequence reads were phylogenetically classified. Similarity of membership and structure in the communities were calculated. At the end of the study, the greatest COO effect was found in coccidia-challenged broilers, with an OE body weight of 1,889 ± 52.4 g with respect to 1,799 ± 36.2 g for CE (P < 0.01). Broiler cecal samples were consistent in that phylum Firmicutes and class Clostridia were highly prevalent; COO had no effect on these taxa levels between the 4 treatments (P > 0.05). A positive correlation (P < 0.01) was observed between the Firmicutes:Bacteriodetes phyla ratio against body weight at 35 D of age. This study provided both positive and negative correlations between broiler body weight against some bacterial groups identified, offering perspectives regarding bacterial groups and their impact on host health and metabolism. Lippia origanoides Kunth high thymol content showed a beneficial effect on body weight and the feed conversion ratio in broilers under coccidia challenge.

Correlation between Jejunal Microbial Diversity and Muscle Fatty Acids Deposition in Broilers Reared at Different Ambient Temperatures

Temperature, which is an important environmental factor in broiler farming, can significantly influence the deposition of fatty acids in muscle. 300 one-day-old broiler chicks were randomly divided into three groups and reared at high, medium and low temperatures (HJ, MJ and LJ), respectively. Breast muscle and jejunal chyme samples were collected and subjected to analyses of fatty acid composition and 16S rRNA gene sequencing. Through spearman’s rank correlation coefficient, the data were used to characterize the correlation between jejunal microbial diversity and muscle fatty acid deposition in the broilers. The results showed that Achromobacter, Stenotrophomonas, Pandoraea, Brevundimonas, Petrobacter and Variovorax were significantly enriched in the MJ group, and all of them were positively correlated with the fatty acid profiling of muscle and multiple lipid metabolism signaling pathways. Lactobacillus was significantly enriched in the HJ group and exhibited a positive correlation with fatty acid deposition. Pyramidobacter, Dialister, Bacteroides and Selenomonas were significantly enriched in the LJ group and displayed negative correlation with fatty acid deposition. Taken together, this study demonstrated that the jejunal microflora manifested considerable changes at high and low ambient temperatures and that jejunal microbiota changes were correlated with fatty acid deposition of muscle in broilers.

Occurrence of Soil Fungi in Antarctic Pristine Environments

The presence of fungi in pristine Antarctic soils is of particular interest because of the diversity of this microbial group. However, the extreme conditions that coexist in Antarctica produce a strong selective pressure that could lead to the evolution of novel mechanisms for stress tolerance by indigenous microorganisms. For this reason, in recent years, research on cold-adapted microorganisms has increased, driven by their potential value for applications in biotechnology. Cold-adapted fungi, in particular, have become important sources for the discovery of novel bioactive secondary metabolites and enzymes. In this study, we studied the fungal community structure of 12 soil samples from Antarctic sites, including King George Island (including Collins Glacier), Deception Island and Robert Island. Culturable fungi were isolated and described according to their morphological and phenotypical characteristics, and the richness index was compared with soil chemical properties to describe the fungal community and associated environmental parameters. We isolated 54 fungal strains belonging to the following 19 genera: Penicillium, Pseudogymnoascus, Lambertella, Cadophora, Candida, Mortierella, Oxygenales, Geomyces, Vishniacozyma, Talaromyces, Rhizopus, Antarctomyces, Cosmospora, Tetracladium, Leptosphaeria, Lecanicillium, Thelebolus, Bjerkandera and an uncultured Zygomycete. The isolated fungi were comprised of 70% Ascomycota, 10% Zygomycota, 10% Basidiomycota, 5% Deuteromycota and 5% Mucoromycota, highlighting that most strains were associated with similar genera grown in cold environments. Among the culturable strains, 55% were psychrotrophic and 45% were psychrophilic, and most were Ascomycetes occurring in their teleomorph forms. Soils from the Collins Glacier showed less species richness and greater species dominance compared with the rest of the sites, whereas samples 4, 7, and 10 (from Fildes Bay, Coppermine Peninsula and Arctowski Station, respectively) showed greater species richness and less species dominance. Species richness was related to the C/N ratio, whereas species dominance was inversely related to C and N content. Thus, the structure of the fungal community was mainly related to soil chemical parameters more than sample location and altitude.

In vitro inhibition of Eimeria tenella sporozoite invasion into host cells by probiotics

The aim was to study the effects of probiotics isolated from the intestinal tract of livestock animals on Eimeria tenella invasion into Madin-Darby bovine kidney (MDBK) cells in vitro. E. tenella sporozoites were purified and labeled with 5(6)-carboxyfluorescein diacetate N-succinimidyl ester before seeding on cell cultures, and invasion was evaluated by fluorescence microscopy. Two protocols (A and B) were used. In protocol A, Enterococcus faecium # 589 or Lactobacillus salivarius subsp. salivarius # 505 were added together with sporozoites to MDBK cell cultures and invasion was evaluated after incubation for approximately 20h. Viable, dead, or spent culture supernatants of probiotics were tested. In protocol B, viable probiotics were incubated with MDBK cells for one hour before sporozoites were added and invasion was evaluated after two more hours of incubation. Parasite invasion of viable, dead, or spent culture supernatant of E. faecium # 589 was assessed. Using protocol A, it was shown that parasite invasion was inhibited by viable (80%) or dead (75%) E. faecium # 589. While inhibition by viable L. salivarius subsp. salivarius # 505 was not valid at the highest concentration and not significant at the other test concentrations, dead cells inhibited parasite invasion up to 45%. Spent culture supernatants of both probiotics had no influence on parasite invasion. Using protocol B, it was shown that viable Bifidobacterium animalis subsp. animalis # 503, E. faecium # 497, E. faecium # 589, L. reuteri # 514, L. salivarius subsp. salivarius # 505, and Bacillus subtilis # 588 inhibited parasite invasion into MDBK cells up to 80%. Anticoccidial activity was strain-specific for E. faecium strains, and the strongest effect was shown by E. faecium # 589. Anticoccidial effects of some of the tested probiotics have already been shown in vivo, which makes them candidates to prevent coccidiosis. These findings have now been confirmed in vitro. The used parasite invasion assay is a fast and inexpensive tool to screen probiotics for prevention of coccidiosis.

Molecular analysis of the caecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic

The gastrointestinal tract commensal microbiome is important for host nutrition, health and immunity. Little information is available regarding the role of these commensals at other mucosal surfaces in poultry. Tracheal mucosal surfaces offer sites for first-line health and immunity promotion in broilers, especially under stress-related conditions. The present study is aimed at elucidating the effects of feed supplementations with mannanoligosaccharides (MOS) prebiotic and a probiotic mixture (PM) on the caecal and tracheal microbiome of broilers kept under chronic heat stress (HS; 35 ± 2°C). Day-old chickens were randomly divided into five treatment groups: thermoneutral control (TN-CONT), HS-CONT, HS-MOS, HS-PM and HS synbiotic (fed MOS and PM). Caecal digesta and tracheal swabs were collected at day 42 and subjected to DNA extraction, followed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. The PCR-DGGE dendrograms revealed significant (49.5% similarity coefficients) differences between caecal and tracheal microbiome. Tracheal microbiome pyrosequencing revealed 9 phyla, 17 classes, 34 orders, 68 families and 125 genera, while 11 phyla, 19 classes, 34 orders, 85 families and 165 genera were identified in caeca. An unweighted UniFrac distance metric revealed a distinct clustering pattern (analysis of similarities, P = 0.007) between caecal and tracheal microbiome. Lactobacillus was the most abundant genus in trachea and caeca and was more abundant in caeca and trachea of HS groups compared with the TN-CONT group. Distinct bacterial clades occupied the caecal and tracheal microbiomes, although some bacterial groups overlapped, demonstrating a core microbiome dominated by Lactobacillus. No positive effects of supplementations were observed on abundance of probiotic bacteria.

Dietary Capsicum and Curcuma longa oleoresins increase intestinal microbiome and necrotic enteritis in three commercial broiler breeds

Three commercial broiler breeds were fed from hatch with a diet supplemented with Capsicum and Curcuma longa oleoresins, and co-infected with Eimeria maxima and Clostridium perfringens to induce necrotic enteritis (NE). Pyrotag deep sequencing of bacterial 16S rRNA showed that gut microbiota compositions were quite distinct depending on the broiler breed type. In the absence of oleoresin diet, the number of operational taxonomic units (OTUs), was decreased in infected Cobb, and increased in Ross and Hubbard, compared with the uninfected. In the absence of oleoresin diet, all chicken breeds had a decreased Candidatus Arthromitus, while the proportion of Lactobacillus was increased in Cobb, but decreased in Hubbard and Ross. Oleoresin supplementation of infected chickens increased OTUs in Cobb and Ross, but decreased OTUs in Hubbard, compared with unsupplemented/infected controls. Oleoresin supplementation of infected Cobb and Hubbard was associated with an increased percentage of gut Lactobacillus and decreased Selenihalanaerobacter, while Ross had a decreased fraction of Lactobacillus and increased Selenihalanaerobacter, Clostridium, Calothrix, and Geitlerinema. These results suggest that dietary Capsicum/Curcuma oleoresins reduced the negative consequences of NE on body weight and intestinal lesion, in part, through alteration of the gut microbiome in 3 commercial broiler breeds.

Evaluation of the efficacy of sequential or continuous administration of probiotics and phytogenics in broiler diets

Three dietary combinations of probiotics and phytogenics administered sequentially or continuously were assessed for their effects on broiler performance, nutrient digestibility, caecal microbiota composition, volatile fatty acid (VFA) pattern and plasma total antioxidant capacity (TAC). One-day-old Cobb male broilers (n = 525) were allocated to five experimental treatments for 42 days. Each treatment had three replicates of 35 broilers each. Depending on the time-frame of sequential or continuous addition in the basal diet (BD) of the probiotics (108 CFU/kg BD) and phytogenics (125 mg/kg BD), experimental treatments were: control (no additions, Days 1–42); PE1, probiotic Days 1–14 and phytogenic Days 15–42; PE2, probiotic Days 1–28 and phytogenic Days 29–42; PE3, probiotic and phytogenic continuously (Days 1–42); and A (2.5 mg avilamycin/kg diet, Days 1–42). There was no loss of probiotic viability upon mixing with the phytogenic for up to 7 days. Overall bodyweight gain was higher (P = 0.025) in the control and PE1 than PE2 and PE3, whereas Treatment A was intermediate and not different from the rest. Overall feed intake in the control was the highest (P = 0.003). Treatments PE1, PE2 and PE3 had better (P = 0.004) overall feed conversion ratio (FCR) than the control. The FCR in PE1 and PE3 did not differ from A, which had the best FCR. Mortality did not differ among treatments. Nutrient digestibility and caecal microbiota composition did not differ among treatments. However, differences (P ≤ 0.05) in caecal VFA pattern were noted, with the control having the lowest acetate molar ratio as well as the highest sum of valeric, hexanoic and heptanoic acids. Plasma TAC in the control was lower than in PE3, PE1 and PE2 at Day 14 (P < 0.001) and PE1 (P = 0.003) at Day 42. The concept of sequential or throughout probiotic and phytogenic administration showed promising results regarding feed efficiency and plasma TAC.

Effect of dietary inclusion level of a multi-species probiotic on broiler performance and two biomarkers of their caecal ecology

The effect of the dietary inclusion level of a three-species probiotic on broiler performance, nutrient digestibility, caecal microbiota composition and volatile fatty acid (VFA) pattern was evaluated. Day-old Cobb broilers (n = 448) were allocated in four treatments for 6 weeks. Each treatment had four replicates (two per gender) of 28 broilers each. Depending on the type of addition per kg basal diet, treatments were C (no other addition), PL (108 colony forming units of probiotic), PH (109 colony forming units of probiotic) and A (2.5 mg avilamycin). Overall bodyweight gain was better (P = 0.002) in PL and PH than in the control (2082 g) by 8.7% and 7.5%, respectively, while treatment PL did not differ from A (2341 g), which showed the highest bodyweight gain. The ileal and total-tract apparent digestibility of DM and the apparent metabolisable energy content corrected for N improved linearly (P ≤ 0.05) with the probiotic level. Fluorescent in situ hybridisation analysis showed caecal Bifidobacterium levels to increase linearly (P = 0.006) with the probiotic level. Probiotic administration resulted in altered caecal VFA patterns compared with the control. Gender effects (P ≤ 0.05) were noted for caecal levels of C. histolyticum group, Bacteroides fragilis group and Streptococcus spp., while interactions (P ≤ 0.05) of treatment with gender were seen for Bifidobacterium and all VFA components, except for acetate. In conclusion, beneficial effects on bodyweight gain, DM digestibility, apparent metabolisable energy content corrected for N, caecal Bifidobacterium levels and VFA patterns were noted with both probiotic inclusion levels.

Comparative evaluation of probiotic and salinomycin effects on performance and coccidiosis control in broiler chickens

The annual financial loss to the poultry industry as a result of coccidiosis has been estimated at about US $3 billion. The objective of this study was to evaluate and compare the effects of probiotics and salinomycin as feed additives on performance and coccidiosis control in male broilers raised to 42 d of age. The study consisted of 360 Cobb male broiler chickens randomly allocated to 4 groups each with 3 replicates. Group 1: untreated, unchallenged negative control group (NC); group 2: untreated, challenged positive control group (PC); group 3: negative control supplemented with salinomycin 66 mg/kg, challenged group (Sal); and group 4: negative control supplemented with probiotics, challenged (Prob mix). On d 15, all birds (except group 1) were challenged with approximately 75,000, 25,000, and 75,000 of Eimeria acervulina, Eimeria maxima, and Eimeria tenella oocytes, respectively, that were mixed into the feed. Feed conversion ratio and mortality were recorded throughout the experiment. On d 21 and 42, intestinal lesions and litter conditions were scored. On d 7, 14, 21, 28, 35, and 42, oocyst counts were determined from 10 freshly collected fecal samples per pen. The results showed that mortality, litter, and lesion scores at d 21 and 42, and oocyst shedding at d 21 did not differ significantly between the Prob mix and the Sal groups. However on d 28, oocyst shedding was significantly lower in the Sal group than in the PC group but insignificantly lower than the Prob mix group. Body weights of the Prob mix group at d 42 were significantly lower than the Sal group; however, the feed conversion ratio values were similar between the 2 groups. The results of this study showed that probiotics supplementation could be considered as a potential strategy to control coccidiosis in broiler chickens.

The poultry-associated microbiome: network analysis and farm-to-fork characterizations

Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2-4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Background

In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems.

Results

PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10′000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63±18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes.

Conclusions

PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.