Bacterial Tag-encoded FLX Amplicon Pyrosequencing Research Articles

Impacts of a glyphosate-based herbicide on the gut microbiome of three earthworm species (Alma millsoni, Eudrilus eugeniae and Libyodrilus violaceus): A pilot study.

While the impact of glyphosate-based herbicides (GBHs) on earthworms has been studied, little is known about their effects on the earthworm gut microbiome. This study investigated the impact of a GBH on the gut microbial communities of three earthworm species (Alma millsoni, Eudrilus eugeniae and Libyodrilus violaceus). Earthworm species accommodated in soil were sprayed with 115.49 mL/m² of Roundup® Alphée or water. Gut microbiome composition was analysed using 16S rRNA Bacterial Tag-Encoded FLX Amplicon Pyrosequencing (bTEFAP) at the 8th week post-herbicide application. A profound shift in bacterial populationswas observed in all exposed earthworms with Proteobacteria becoming the dominant phylum. Affected bacteria were mostly from the genus Enterobacter, Pantoea and Pseudomonas, which together represented approximately 80 % of the total abundance assigned at the genus level in exposed earthworms, while they were present at a minor abundance (∼1%) in unexposed earthworms. Although consistent results were observed between the three groups of worm species, it is not possible to generalize these outcomes due to a lack of biological replicates, which does not allow for inferential statistical analysis. Nevertheless, our study is the first to report the effects of a GBH on the earthworm gut microbiome and paves the way for future more comprehensive investigations.

PSIX-2 Potential role of rumen microbiota in altering average daily gain and feed efficiency in meat goats fed simple and mixed pastures using bacterial tag-encoded FLX amplicon pyrosequencing

Abstract Our objective was to examine whether the comparative abundance of the Bacteroidetes (B) and Firmicutes (F) bacterial phyla in meat goats fed simple and mixed forages influenced average daily gain (ADG), rumen fermentation parameters and bacterial diversity changes using a tag-encoded FLX amplicon pyrosequencing (bTEFAP). Thirty-six Kiko-cross growing meat goats (BW = 27.7 ± 2.83) at approximate age of 7 mo were used in this study. Animals were randomly allocated to three pasture treatment groups (n = 12) as follows: (1) bermudagrass (BG; Cynodon dactylon), (2) sun hemp (SH; Crotalaria juncea) forage, and (3) BG + SH forage combinations for 45-d. Results indicated that there were no differences in initial BW among treatments, but final BW and ADG were higher (P < 0.01) for SH and BG + SH combinations than for BG alone. We investigated the alterations between the different forage diets and found that ADG and rumen fermentation (A/P ratio), were highly correlated with the abundance of various bacterial populations within the rumen microbiome. There were linear decreases in percentage of Bacteroidetes (R2 = -0.84; P < 0.05) associated with decreasing ADG. In contrast, increased ADG was linearly associated with higher percentages of Firmicutes (R2 = 0.79; P < 0.05), F/B ratio (R2 = 0.88; P = 0.07), total VFA (R2 = 0.45; P < 0.05), and lower A/P ratio (R2 = -0.72; P < 0.01). This suggest that the substrate and bacterial community have the role in adapting host biological parameters in meat goats. The abundance examination of both Bacteroidetes and Firmicutes will be useful for exploring the structure of gut microbiota as an estimate of animal performance.

Metagenomic analysis of microbial community associated with coral mucus from the Gulf of Aqaba

Coral-associated microbial communities contribute to a wide variety of useful roles regarding the their host, and therefore, the arrangement of the general microbiome network can emphatically impact coral wellbeing and survival. Various pollution sources can interfere and disrupt the microbial relationship with corals. Here, we adopted the bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP®) technique to investigate the shift of microbial communities associated with the mucus of the coral Stylophora pistillata collected from five sites (Marine Science Station, Industrial Complex, Oil Terminal, Public Beach, and Phosphate Port) along the Gulf of Aqaba (Red Sea). Our results revealed a high diversity in bacterial populations associated with coral mucus. Proteobacteria were observed to be the dominating phylum among all sampling sites. The identified bacterial taxa belong to the pathogenic bacteria from the genus Vibrio was presented in varying abundances at all sampling sites. Diversity and similarity analysis of microbial communists based on rarefaction curve and UniFrac cluster respectively demonstrated that there are variances in microbial groups associated with coral mucus along sites. The pollution sources among different locations along the Gulf of Aqaba seem to affect the coral-associated holobiont leading to changes in bacterial populations due to increasing human activities.

Potential role of rumen microbiota in altering average daily gain and feed efficiency in meat goats fed simple and mixed pastures using bacterial tag-encoded FLX amplicon pyrosequencing1.

Cost-effective and feasible production system of meat goats requires that grazed forages are converted to profitable goat meat product. However, there are studies as how altering forage type influences ruminal fermentation parameters and animal growth performance, and interact with microbiota in meat goats. Our objective for current study was to examine whether the comparative abundance of the Bacteroidetes (B) and Firmicutes (F) bacterial phyla in meat goats fed simple and mixed forages influenced average daily gain (ADG) and rumen fermentation parameters. In the present study, a molecular approach, bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) was applied to accomplish diversity analyses of rumen bacterial populations. Thirty-six Kiko-cross growing meat goats (body weight (BW) = 27.7 ± 2.83 kg) at approximately 7 mo of age were used in this study. Animals were randomly allocated to 3 pasture treatment groups (n = 12) as follows: 1) bermudagrass pasture (BG; Cynodon dactylon), 2) sunn hemp forage (SH; Crotalaria juncea), and 3) BG + SH forage combinations. There were 2 replicates per treatment and animals grazed these pastures for 45 d. Results indicated that treatments had similar initial BW, but final BW and ADG were higher (P < 0.01) for SH and BG + SH combinations than for BG alone. Animal ADG and rumen fermentation (acetate to propionate; A/P ratios) were highly correlated with the abundance of various bacterial populations within the rumen microbiome. There were linear decreases in percentage of Bacteroidetes (R2 = -0.84; P < 0.05) associated with decreasing ADG. In contrast, increased ADG was linearly associated with higher percentages of Firmicutes (R2 = 0.79; P < 0.05), F/B ratios (R2 = 0.88; P = 0.07), total VFA (R2 = 0.45; P < 0.05), and lower A/P ratio (R2 = -0.72; P < 0.01). This suggests that the substrates (diets) and bacterial community have the role in adapting host biological parameters in meat goats. The abundance examination of both Bacteroidetes and Firmicutes will be useful for exploring the structure of gut microbiota as an estimate of animal performance.

The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes.

The bacterial microbiome in chronic rhinosinusitis (CRS) remains poorly understood. Microorganisms are believed to be important contributors to the inflammatory response seen in these patients. To examine the bacterial CRS microbiome by using a pyrosequencing technique and determine the diversity, richness, prevalence, and abundance of bacterial species in these patients. Furthermore, the postoperative changes that occur in the microbiome and correlations with patient outcomes are assessed. Swabs were collected from 23 patients with CRS and 11 controls during surgery. Further postoperative swabs were collected in the CRS group. Bacterial DNA was extracted from the swabs and then sequenced by using 16S ribosomal DNA bacterial tag-encoded FLX amplicon pyrosequencing. A total of 456 unique bacterial species were detected. No difference was seen for richness or diversity between the study groups (p > 0.05). Diversity declined after surgery in the CRS group (p = 0.01). Propionibacterium acnes and Staphylococcus epidermidis were the most prevalent species. Several significant differences were determined for prevalence and mean relative abundance (MRA) between the study groups. In particular, Acinetobacter johnsonii was more prevalent and had a higher MRA in the controls. Furthermore, the MRA of this species increased after surgery and was associated with improved quality of life. This study characterized the sinonasal microbiome in a group of controls and patients with CRS. Important differences in diversity, prevalence, abundance, and temporal changes were described. Of great interest is the potential association between A. johnsonii and health. These findings provide new insights into the interplay between the microbiome and health in the paranasal sinuses.

Metagenomic data of the bacterial community in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252).

The data in this article includes the sequences of bacterial 16S rRNA gene from metagenome of Macondo oil (MC252)-treated and non-oil-treated sediment microcosms, collected from coastal Gulf of Mexico and Bayou La Batre, USA. Metacommunity DNA was PCR amplified with 341F and 907R oligonucleotide primers, targeting V3–V5 regions of the 16S rRNA gene. Data were generated by using bacterial tag-encoded FLX-amplicon pyrosequencing (bTEFAP) methodology and then processed using bioinformatics tools such as QIIME. The data information is deposited to NCBI׳s BioProject and BioSample and raw sequence files are available via NCBI׳s Sequence Read Archive (SRA) database.

Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy

Hospital-associated infections cause considerable morbidity and mortality, and are expensive to treat. Organisms causing these infections can be sourced from the inanimate environment around a patient. Could the difficulty in eradicating these organisms from the environment be because they reside in dry surface biofilms? The intensive care unit (ICU) of a tertiary referral hospital was decommissioned and the opportunity to destructively sample clinical surfaces was taken in order to investigate whether multidrug-resistant organisms (MDROs) had survived the decommissioning process and whether they were present in biofilms. The ICU had two 'terminal cleans' with 500 ppm free chlorine solution; items from bedding, surrounds, and furnishings were then sampled with cutting implements. Sections were sonicated in tryptone soya broth and inoculated on to chromogenic plates to demonstrate MDROs, which were confirmed with the Vitek2 system. Genomic DNA was extracted directly from ICU samples, and subjected to polymerase chain reaction (PCR) for femA to detect Staphylococcus aureus and the microbiome by bacterial tag-encoded FLX amplicon pyrosequencing. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) were performed on environmental samples. Multidrug-resistant bacteria were cultured from 52% (23/44) of samples cultured. S. aureus PCR was positive in 50%. Biofilm was demonstrated in 93% (41/44) of samples by CLSM and/or SEM. Pyrosequencing demonstrated that the biofilms were polymicrobial and contained species that had multidrug-resistant strains. Dry surface biofilms containing MDROs are found on ICU surfaces despite terminal cleaning with chlorine solution. How these arise and how they might be removed requires further study.

Crustose coralline algal species host distinct bacterial assemblages on their surfaces.

Crustose coralline algae (CCA) are important components of many marine ecosystems. They aid in reef accretion and stabilization, create habitat for other organisms, contribute to carbon sequestration and are important settlement substrata for a number of marine invertebrates. Despite their ecological importance, little is known about the bacterial communities associated with CCA or whether differences in bacterial assemblages may have ecological implications. This study examined the bacterial communities on four different species of CCA collected in Belize using bacterial tag-encoded FLX amplicon pyrosequencing of the V1-V3 region of the 16S rDNA. CCA were dominated by Alphaproteobacteria, Gammaproteobacteria and Actinomycetes. At the operational taxonomic unit (OTU) level, each CCA species had a unique bacterial community that was significantly different from all other CCA species. Hydrolithon boergesenii and Titanoderma prototypum, CCA species that facilitate larval settlement in multiple corals, had higher abundances of OTUs related to bacteria that inhibit the growth and/or biofilm formation of coral pathogens. Fewer coral larvae settle on the surfaces of Paragoniolithon solubile and Porolithon pachydermum. These CCA species had higher abundances of OTUs related to known coral pathogens and cyanobacteria. Coral larvae may be able to use the observed differences in bacterial community composition on CCA species to assess the suitability of these substrata for settlement and selectively settle on CCA species that contain beneficial bacteria.

Cultivation-independent comprehensive survey of bacterial diversity in Tulsi Shyam Hot Springs, India.

A taxonomic description of bacteria was deduced from 5.78 Mb metagenomic sequence retrieved from Tulsi Shyam hot spring, India using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Metagenome contained 10,893 16S rDNA sequences that were analyzed by MG-RAST server to generate the comprehensive profile of bacteria. Metagenomic data are available at EBI under EBI Metagenomics database with accession no. ERP009559. Metagenome sequences represented the 98.2% bacteria origin, 1.5% of eukaryotic and 0.3% were unidentified. A total of 16 bacterial phyla demonstrating 97 families and 287 species were revealed in the hot spring metagenome. Most abundant phyla were Firmicutes (65.38%), Proteobacteria (21.21%) and unclassified bacteria (10.69%). Whereas, Peptostreptococcaceae (37.33%), Clostridiaceae (23.36%), and Enterobacteriaceae (16.37%) were highest reported families in metagenome. Ubiquitous species were Clostridium bifermentans (17.47%), Clostridium lituseburense (13.93%) and uncultured bacterium (10.15%). Our data provide new information on hot spring bacteria and shed light on their abundance, diversity, distribution and coexisting organisms.

Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP) based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India.

Bacterial diversity and archaeal diversity in metagenome of the Lonar soda lake sediment were assessed by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Metagenome comprised 5093 sequences with 2,531,282 bp and 53 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA218849. Metagenome sequence represented the presence of 83.1% bacterial and 10.5% archaeal origin. A total of 14 different bacteria demonstrating 57 species were recorded with dominating species like Coxiella burnetii (17%), Fibrobacter intestinalis (12%) and Candidatus Cloacamonas acidaminovorans (11%). Occurrence of two archaeal phyla representing 24 species, among them Methanosaeta harundinacea (35%), Methanoculleus chikugoensis (12%) and Methanolinea tarda (11%) were dominating species. Significant presence of 11% sequences as an unclassified indicated the possibilities for unknown novel prokaryotes from the metagenome.

First Evidence for the Presence of Iron Oxidizing Zetaproteobacteria at the Levantine Continental Margins

During the 2010–2011 E/V Nautilus exploration of the Levantine basin’s sediments at the depth of 300–1300 m, densely patched orange-yellow flocculent mats were observed at various locations along the continental margin of Israel. Cores from the mat and the control locations were collected by remotely operated vehicle system (ROV) operated by the E/V Nautilus team. Microscopic observation and phylogenetic analysis of microbial 16S and 23S rRNA gene sequences indicated the presence of zetaproteobacterial stalk forming Mariprofundus spp. – like prokaryotes in the mats. Bacterial tag-encoded FLX amplicon pyrosequencing determined that zetaproteobacterial populations were a dominant fraction of microbial community in the biofilm. We show for the first time that zetaproteobacterial may thrive at the continental margins, regardless of crustal iron supply, indicating significant fluxes of ferrous iron to the sediment-water interface. In light of this discovery, we discuss the potential bioavailability of sediment-water interface iron for organisms in the overlying water column.

Bacterial diversity within five unexplored freshwater lakes interconnected by surface channels in East Antarctic Dronning Maud Land (Schirmacher Oasis) using amplicon pyrosequencing

The Schimacher Oasis, an ice-free plateau in East Antarctic Dronning Maud Land, consists of over 120 freshwater lakes. These lakes are connected largely through four major surface channels. The bacterial diversity in these lake ecosystems remains largely unexplored. In this study, we compared the bacterial diversity in five freshwater lakes (L42, L46, L47, L50, and L51) interconnected by two surface channels using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) method. We further compared the resultant bacterial composition from these five lakes with another freshwater lake in the Schirmacher Oasis, Lake Tawani(P), which is not connected through the same surface channels. Using bTEFAP, we differentiated nine different phyla with the phyla Proteobacteria (especially the class Alphaproteobacteria) and Bacteroidetes (the class Sphingobacteria) dominating in lakes interconnected by surface channel 1, while the phyla Chloroflexi and Firmicutes were highly abundant in lakes interconnected by surface channel 2. The operational taxonomic unit (OTU) network and Principle Coordinate Analysis (PCoA) plot based on unweighted UNIFRAC determined that the bacterial assemblages found in these five lakes are different than the bacterial composition residing in Lake Tawani(P). The distribution and the diversity of the bacterial communities in Schirmacher Oasis freshwater lakes that are connected through surface channels may provide an insight into the role of the extreme physico-chemical parameters that help shape microbially driven functional ecosystems in other oases on this icy continent.

Gastrointestinal Bacterial and Methanogenic Archaea Diversity Dynamics Associated with Condensed Tannin-Containing Pine Bark Diet in Goats Using 16S rDNA Amplicon Pyrosequencing

Eighteen Kiko-cross meat goats (n = 6) were used to collect gastrointestinal (GI) bacteria and methanogenic archaea for diversity measures when fed condensed tannin-containing pine bark (PB). Three dietary treatments were tested: control diet (0% PB and 30% wheat straw (WS); 0.17% condensed tannins (CT) dry matter (DM)); 15% PB and 15% WS (1.6% CT DM), and 30% PB and 0% WS (3.2% CT DM). A 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing technique was used to characterize and elucidate changes in GI bacteria and methanogenic archaea diversity among the diets. Proteobacteria was the most dominant phylum in goats with mean relative abundance values ranging from 39.7 (30% PB) to 46.5% (control) and 47.1% (15% PB). Other phyla individually accounted for fewer than 25% of the relative abundance observed. Predominant methanogens were Methanobrevibacter (75, 72, and 49%), Methanosphaera (3.3, 2.3, and 3.4%), and Methanobacteriaceae (1.2, 0.6, and 0.7%) population in control, 15, and 30% PB, respectively. Among methanogens, Methanobrevibacter was linearly decreased (P = 0.05) with increasing PB supplementation. These results indicate that feeding PB selectively altered bacteria and methanogenic archaeal populations in the GI tract of goats.

Low-Level Detection ofCandidatusLiberibacter Solanacearum inBactericera cockerelli(Hemiptera: Triozidae) by 16s rRna Pyrosequencing: Table 1.

Accurate detection and quantification of Candidatus Liberibacter solanacearum (CLs), the putative causal agent of zebra chip disease of potato (Solanum tuberosum L.), in the potato psyllid, Bactericera cockerelli (Sulc), has become necessary to better understand the biology of the disease cycle. Studies on the transmission efficiency of potato psyllids have shown inconsistencies with field surveys. There have also been reports of laboratory colonies inexplicably losing and regaining CLs infection as detected by polymerase chain reaction (PCR). Until now, DNA primers were used to detect CLs in potato psyllid tissue using conventional polymerase chain reaction (PCR) and gel electrophoresis or by real-time quantitative PCR. In this study, CLs was detected using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) at levels identifiable by PCR, and low levels, including samples with only one cell of CLs. Potato psyllids with <300 pyrosequencing reads did not show positive using conventional PCR. These results indicate that the currently accepted PCR diagnostic technique produces false negatives due to detection limits higher than what is generally present in field collected psyllids, and also provides an explanation as to why laboratory colonies seem to lose and regain CLs infection.

Operational aspects, pH transition and microbial shifts of a H2S desulfurizing biotrickling filter with random packing material

Pall rings, a common random packing material, were used in the biotrickling filtration of biogas with high H2S. Assessment of 600d of operation covered the reactor start-up, the operation at neutral pH and the transition from neutral to acid pH. During the start-up period, operational parameters such as the aeration rate and the trickling liquid velocity were optimized. During the steady-state operation at neutral pH, the performance of the random packing material was investigated by reducing the gas contact time at both constant and increasing H2S loads. The random packing material showed similar elimination capacities and removal efficiencies in comparison with previous studies with a structured packing material, indicating that Pall rings are suitable for biogas desulfurization in biotrickling filters. The diversity of Eubacteria and the structure of the community were investigated before and after the pH transition using the bacterial tag-encoded FLX amplicon pyrosequencing. The pH transition to acid pH drastically reduced the microbial diversity and produced a progressive specialization of the sulfur-oxidizing bacteria community without any detrimental effect on the overall desulfurizing capacity of the reactor. During acidic pH operation, a persistent accumulation of elemental sulfur was found.

Microbial Diversity and Phylogeny Analysis of Buttermilk, a Fermented Milk Product, Employing 16S rRNA-Based Pyrosequencing

Buttermilk is a traditional fermented dairy product popular in India and other Asian countries. In this study, the microbial population in a buttermilk sample was investigated by 16S rRNA gene-based bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) approach. A total of 23,080 high-quality pyrosequencing reads was obtained. Of these, 96.3% of reads represented the well-defined domain bacteria and 3.7% represented unclassified domain; no archaeal sequences were found. Lactobacillus delbrueckii was the most predominant species identified, which constituted 94.86% of total reads. The other minor genera found included Streptococcus, Aeromonas, Methylobacter, Enterococcus, Micrococcus, Ralstonia, Moraxella, and Flavobacter. The buttermilk did not contain any pathogenic species. However, the roles of unclassifiable organisms are yet to be studied.

A high-throughput microfluidic dental plaque biofilm system to visualize and quantify the effect of antimicrobials

Few model systems are amenable to developing multi-species biofilms in parallel under environmentally germane conditions. This is a problem when evaluating the potential real-world effectiveness of antimicrobials in the laboratory. One such antimicrobial is cetylpyridinium chloride (CPC), which is used in numerous over-the-counter oral healthcare products. The aim of this work was to develop a high-throughput microfluidic system that is combined with a confocal laser scanning microscope (CLSM) to quantitatively evaluate the effectiveness of CPC against oral multi-species biofilms grown in human saliva. Twenty-four-channel BioFlux microfluidic plates were inoculated with pooled human saliva and fed filter-sterilized saliva for 20 h at 37°C. The bacterial diversity of the biofilms was evaluated by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). The antimicrobial/anti-biofilm effect of CPC (0.5%-0.001% w/v) was examined using Live/Dead stain, CLSM and 3D imaging software. The analysis of biofilms by bTEFAP demonstrated that they contained genera typically found in human dental plaque. These included Aggregatibacter, Fusobacterium, Neisseria, Porphyromonas, Streptococcus and Veillonella. Using Live/Dead stain, clear gradations in killing were observed when the biofilms were treated with CPC between 0.5% and 0.001% w/v. At 0.5% (w/v) CPC, 90% of the total signal was from dead/damaged cells. Below this concentration range, less killing was observed. In the 0.5%-0.05% (w/v) range CPC penetration/killing was greatest and biofilm thickness was significantly reduced. This work demonstrates the utility of a high-throughput microfluidic-CLSM system to grow multi-species oral biofilms, which are compositionally similar to naturally occurring biofilms, to assess the effectiveness of antimicrobials.

Coaggregation occurs amongst bacteria within and between biofilms in domestic showerheads

Showerheads support the development of multi-species biofilms that can be unsightly, produce malodor, and may harbor pathogens. The outer-surface spray-plates of many showerheads support visible biofilms that likely contain a mixture of bacteria from freshwater and potentially from human users. Coaggregation, a mechanism by which genetically distinct bacteria specifically recognize one another, may contribute to the retention and enrichment of different species within these biofilms. The aim of this work was to describe the bacterial composition of outer spray-plate biofilms of three domestic showerheads and to determine the intra- and inter-biofilm coaggregation ability of each culturable isolate. The bacterial composition of the three biofilms was determined by using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) and by culturing on R2A medium. An average of 31 genera per biofilm were identified using bTEFAP and a total of 30 isolates were cultured. Even though the microbial diversity of each showerhead biofilm differed, every cultured isolate was able to coaggregate with at least one other isolate from the same or different showerhead biofilm. Promiscuous coaggregating isolates belonged to the genera Brevundimonas, Micrococcus, and Lysobacter. This work suggests that coaggregation may be a common feature of showerhead biofilms. Characterization of the mechanisms mediating coaggregation, and the inter-species interactions they facilitate, may allow for novel strategies to inhibit biofilm development.

Molecular Characterisation of Gastrointestinal Microbiota of Children With Autism (With and Without Gastrointestinal Dysfunction) and Their Neurotypical Siblings

Many children with autism spectrum disorders (ASDs) suffer from gastrointestinal problems such as diarrhoea, constipation and abdominal pain. This has stimulated investigations into possible abnormalities of intestinal microbiota in autistic patients. Therefore, we designed this study to identify differences (and/or similarities) in the microbiota of children with autism (without gastrointestinal dysfunction: n = 23; with gastrointestinal dysfunction: n = 28) and their neurotypical siblings (n = 53) who share a similar environment using bacterial tag-encoded FLX amplicon pyrosequencing. Regardless of the diagnosis and sociodemographic characteristics, overall, Firmicutes (70%), Bacteroidetes (20%) and Proteobacteria (4%) were the most dominant phyla in samples. Results did not indicate clinically meaningful differences between groups. The data do not support the hypothesis that the gastrointestinal microbiota of children with ASD plays a role in the symptomatology of ASD. Other explanations for the gastrointestinal dysfunction in this population should be considered including elevated anxiety and self-restricted diets.

Bacterial communities in soil mimic patterns of vegetative succession and ecosystem climax but are resilient to change between seasons

Organism succession during ecosystem development has been researched for aboveground plant communities, however, the associated patterns of change in below-ground microbial communities are less described. In 2008, a study was initiated along a developmental sand-dune soil chronosequence bordering northern Lake Michigan near Wilderness Park (WP). It was hypothesized that soil bacterial communities would follow a pattern of change that is associated with soil, plant, and ecosystem development. This study included 5 replicate sites along 9 soils (n = 45) ranging in age from ∼105 to 4010 years since deposition. Soil bacterial community composition and diversity were studied using bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rRNA gene. Bray–Curtis ordination indicated that bacterial community assembly changed along the developmental soil and plant gradient. The changes were not affected by seasonal differences, despite likely differences in plant root C (e.g. exudates), temperature, and water availability in soil. Soil base cations (Ca, Mg) and pH declined, showing log-linear correlations with soil age (r ∼ 0.83, 0.84 and 0.81; P < 0.01). Bacterial diversity (Simpson's 1/D) declined rapidly during the initial stages of soil development (∼105–450 y) and thereafter (>450 y) did not change. Turnover of plant taxa was also more rapid early during ecosystem development and correlated with bacterial community structural change (P < 0.000001; r = 0.56). It is hypothesized that plants help to drive pedogenic change during early (<450 y) soil development (e.g. pH decline, cation leaching) which drive selection of soil bacterial communities. In mature soils (∼450–4000 y), resilient and stable soil bacterial community structures developed, mimicking steady-state climax communities that were observed during latter stages of primary plant succession. These relationships point to possible feedbacks between plant and bacterial communities during ecosystem development.