Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H
production systems. Despite its importance, there is little information on the ...partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH
). High-throughput sequencing and metagenome functional prediction from 16S rRNA data showed that butyrate production pathways and microbial communities were different during batch (closed) and continuous-mode operation.
,
, and
were the most abundant phylotypes in the closed system without PH
control, whereas
,
, and
were the most abundant phylotypes under continuous operation at low PH
. Putative butyrate producers identified in our system were from
,
,
, and
. Metagenome prediction analysis suggests that nonbutyrogenic microorganisms influenced butyrate production by generating butyrate precursors such as acetate, lactate, and succinate. 16S rRNA gene analysis suggested that, in the reactor, a partnership between identified butyrogenic microorganisms and succinate (i.e.,
), acetate (i.e.,
and
), and lactate producers (i.e.,
and
) took place under continuous-flow operation at low PH
.
This study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system. Bioinformatics analysis allowed us to identify potential butyrogenic phylotypes and associated butyrate metabolism pathways when we systematically varied the PH
in a carefully controlled fermentation system. Our insights may be adapted to butyrate production studies in biohydrogen systems and gut models, since butyrate is a main product and a crucial fatty acid in human/animal colon health.
► Methane production under the specific conditions in Mexico City was demonstrated. ► Enhanced performance was achieved with pH control and nitrogen addition. ► Co-digestion of FVW with meat residues ...allows high and stable performance (30L). ► The microbial population in the AD system during optimal performance was determined. ► Bacterial and Archaea populations were correlated with its function in the AD system.
This study evaluated the feasibility of methane production from fruit and vegetable waste (FVW) obtained from the central food distribution market in Mexico City using an anaerobic digestion (AD) process. Batch systems showed that pH control and nitrogen addition had significant effects on biogas production, methane yield, and volatile solids (VS) removal from the FVW (0.42mbiogas3/kgVS, 50%, and 80%, respectively). Co-digestion of the FVW with meat residues (MR) enhanced the process performance and was also evaluated in a 30L AD system. When the system reached stable operation, its methane yield was 0.25 (m3/kgTS), and the removal of the organic matter measured as the total chemical demand (tCOD) was 65%. The microbial population (general Bacteria and Archaea) in the 30L system was also determined and characterized and was closely correlated with its potential function in the AD system.
ABSTRACT
Niche is a fundamental concept in ecology. It integrates the sum of biotic and abiotic environmental requirements that determines a taxon's distribution. Microbiologists currently lack ...quantitative approaches to address niche-related hypotheses. We tested four approaches for the quantification of niche breadth and overlap of taxa in amplicon sequencing datasets, with the goal of determining generalists, specialists and environmental-dependent distributions of community members. We applied these indices to in silico training datasets first, and then to real human gut and desert biological soil crust (biocrust) case studies, assessing the agreement of the indices with previous findings. Implementation of each approach successfully identified a priori conditions within in silico training data, and we found that by including a limit of quantification based on species rank, one could identify taxa falsely classified as specialists because of their low, sparse counts. Analysis of the human gut study offered quantitative support for Bacilli, Gammaproteobacteria and Fusobacteria specialists enriched after bariatric surgery. We could quantitatively characterise differential niche distributions of cyanobacterial taxa with respect to precipitation gradients in biocrusts. We conclude that these approaches, made publicly available as an R package (MicroNiche), represent useful tools to assess microbial environment-taxon and taxon-taxon relationships in a quantitative manner.
Mathematical indices to quantify niche properties were successfully adapted and applied to microbial taxa, and have been made publicly available as the R package 'MicroNiche'.
We describe the technology and validation of a new whole room indirect calorimeter (WRIC) methodology to quantify volume of methane (VCH
) released from the human body over 24 h concurrently with the ...assessment of energy expenditure and substrate utilization. The new system extends the assessment of energy metabolism by adding CH
, a downstream product of microbiome fermentation that could contribute to energy balance. Our new system consists of an established WRIC combined with the addition of off-axis integrated-cavity output spectroscopy (OA-ICOS) to measure CH
concentration (CH
). Development, validation, and reliability of the system included environmental experiments to measure the stability of the atmospheric CH
, infusing CH
into the WRIC and human cross-validation studies comparing CH
quantified by OA-ICOS and mid-infrared dual-comb spectroscopy (MIR DCS).Our infusion data indicated that the system measured 24-h CH
and VCH
with high sensitivity, reliability, and validity. Cross-validation studies showed good agreement between OA-ICOS and MIR DCS technologies (r = 0.979,
< 0.0001). Human data revealed 24-h VCH
was highly variable between subjects and within/between days. Finally, our method to quantify VCH
released by breath or colon suggested that over 50% of the CH
was eliminated through the breath. The method allows, for the first time, measurement of 24-h VCH
(in kcal) and therefore the measurement of the proportion of human energy intake fermented to CH
by the gut microbiome and released via breath or from the intestine; also, it allows us to track the effects of dietary, probiotic, bacterial, and fecal microbiota transplantation on VCH
.
This is the first time that continuous assessment of CH
is reported in parallel with measurements of O
consumption and CO
production inside a whole room indirect calorimeter in humans and over 24 h. We provide a detailed description of the whole system and its parts. We carried out studies of reliability and validity of the whole system and its parts. CH
is released in humans during daily activities.
Membrane biofilm reactors (MBfRs) deliver gaseous substrates to biofilms that develop on the outside of gas-transfer membranes. When an MBfR delivers electron donors hydrogen (H
2
) or methane (CH
4
...), a wide range of oxidized contaminants can be reduced as electron acceptors, e.g., nitrate, perchlorate, selenate, and trichloroethene. When O
2
is delivered as an electron acceptor, reduced contaminants can be oxidized, e.g., benzene, toluene, and surfactants. The MBfR’s biofilm often harbors a complex microbial community; failure to control the growth of undesirable microorganisms can result in poor performance. Fortunately, the community’s structure and function can be managed using a set of design and operation features as follows: gas pressure, membrane type, and surface loadings. Proper selection of these features ensures that the best microbial community is selected and sustained. Successful design and operation of an MBfR depends on a holistic understanding of the microbial community’s structure and function. This involves integrating performance data with omics results, such as with stoichiometric and kinetic modeling.
Summary
A strictly anaerobic bacterium was isolated from tetrachloroethene (PCE)‐to‐ethene dechlorinating microcosms established with river sediment without prior exposure to chlorinated solvents. ...The isolation procedure included the addition of 2‐bromoethanesulfonate to select against methanogenic archaea, > 50 consecutive 1–2% (v/v) transfers to reduced mineral salts medium amended with trichloroethene (TCE), acetate, and hydrogen, the addition of ampicillin, and the dilution‐to‐extinction principle. Culture‐dependent and 16S rRNA gene‐targeted approaches suggested culture purity. Microscopic examination revealed a homogeneous culture of an organism with a distinct, disc‐shaped morphology. The isolate shared > 99% 16S rRNA gene sequence similarity with members of the Pinellas group of the Dehalococcoides cluster, and was designated Dehalococcoides sp. strain FL2. Strain FL2 could be propagated with TCE, cis‐1,2‐dichloroethene (cis‐DCE), or trans‐DCE as the electron acceptors, acetate as the carbon source, and hydrogen as the electron donor in defined, completely synthetic medium. No other growth‐supporting redox couples were identified. Trichloroethene, cis‐DCE and trans‐DCE were dechlorinated at rates of 27.5, 30.4 and 18.8 µmol l−1 day−1 respectively. Quantitative real‐time polymerase chain reaction (PCR) with a fluorescently labelled linear hybridization probe confirmed growth with these electron acceptors, and suggested that strain FL2 captures energy from both the TCE‐to‐cis‐DCE and 1,2‐DCE‐to‐VC dechlorination steps. Tetrachloroethene and vinyl chloride (VC) were slowly and cometabolically dechlorinated in the presence of a growth‐supporting chloroethene, but ethene formation was incomplete, even after prolonged incubation. At room temperature, strain FL2 grew with a doubling time of 2.4 days, and yielded 166.1 ± 10.2 mg of protein per mole of chloride released. In the presence of excess electron acceptor, strain FL2 consumed hydrogen to a concentration of 0.061 ± 0.016 nM. Dechlorination ceased following the addition of 0.5 mM sulfite, whereas sulfate (10 mM) and nitrate (5 mM) had no inhibitory effects.
The low yield of methane in anaerobic digestion systems represents a loss of energy that can be captured as renewable energy when the input sludge is pre-treated to make it more bioavailable. We ...investigated Focused-Pulsed (FP) pre-treatment, which make complex biological solids more bioavailable by exposing them to rapid pulses of a very strong electric field. We investigated how the microbial ecology in full-scale anaerobic digesters was altered when the digesters' methane production rate was significantly increased by FP pre-treatment. Using clone libraries and quantitative PCR, we demonstrated a shift in methanogenic genera to the acetate-cleaving
Methanosaeta and away from the H
2-oxidizing
Methanoculleus. In addition, the acetate concentration in the effluent was very low, probably due to the dominance of
Methanosaeta, which are capable of scavenging low acetate concentrations. By analyzing 36,797 pyrosequencing tags from the V6 region of the bacterial 16S rRNA gene, along with archaeal and bacterial clone libraries and quantitative PCR, we compared the microbial community composition before and after FP treatment. The
bacterial community became more diverse after FP pre-treatment and was populated more by phylotypes associated with cellulose fermentation (
Ruminococcus), scavenging of biomass-derived organic carbon (
Chloroflexi), and homo-acetogenesis (
Treponema). We interpret that, as the overall activity of the community was stimulated by addition of more bioavailable organic matter, the bacterial community became more phylogenetically diverse to take advantage of the added input of biodegradable material and in response to the more efficient utilization of acetate by
Methanosaeta.
PDF
