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Microorganisms
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Lignocellulose Degradation by Gut Microbiomes, from Mammals to Insects
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Lignocellulose Degradation by Gut Microbiomes, from Mammals to Insects

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 10321

Special Issue Editor

Dr. Alberto Scoma

E-Mail Website
Guest Editor
Head of the Engineered Microbial Systems Laboratory (EMS-Lab), Section of Biological and Chemical Engineering (BCE), Dept. of Engineering, Aarhus University, Aarhus, Denmark
Interests: gut microbiomes; lignocellulose; fermentation; metagenomes; metaproteomes

Special Issue Information

Dear colleagues,

Despite a transition towards a green agenda in recent years, our capacity to sustainably convert renewable feedstocks into platform chemicals of industrial interest is still limited. By green, we here refer to procedures that "reduce or eliminate the use and generation of hazardous substances", as defined in the general principles of Green Chemistry. Renewable chemicals almost entirely depend on biomass, primarily made up of lignocellulose. However, the use of lignocellulose via energy-intensive, toxic-chemical-producing or nonselective physicochemical (pre)treatments is not green, thus not sustainable.

The constant push towards green processes has revived research interest in natural systems. The processes occurring in the gut of herbivorous animals are honed by millions of years of evolution and are naturally green. The essential contribution of gut microbiomes for the degradation of lignocellulose has been historically investigated in ruminants. However, with the rapid development of sequencing techniques, metagenomes and metaproteomes have been recently retrieved from a range of animals: from mammals (e.g., reindeers, zebras, elephants, hippos, giraffes, okapis, rhinos) to insects (e.g., beetles, cockroaches, and most extensively in termites). While contributing to the understanding of the physiology of the hosts, these studies delivered unprecedented information on the potential to deconstruct lignocellulosic material on the part of gut microbiomes.

This Special Issue on “Lignocellulose Degradation by Gut Microbiomes: From Mammals to Insects” aims to collect the most recent findings in the field. Studies should be focused on (but are not restricted to) microbial community assembly; metagenomic, metatranscriptomic and metaproteomics profiles; microbial physiology in incubated samples; and enzymatic assays, in gut microbiomes involved in lignocellulose degradation. This Special Issue also targets: 1) works related to lignocellulose degradation in other types of host–microbiome interactions (e.g., leaf-cutter ants in fungus gardens); and 2) works using gut microbiomes with commercial cellulose, hemicellulose, or lignin as a substrate. Digestibility trials assessing the capacity to ferment plant biomass may be considered, except when exclusively focusing on the health of the host. 

Dr. Alberto Scoma
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gut microbiome
  • lignocellulose
  • fermentation
  • metagenome
  • metaproteome
  • enzymatic assay
  • cellulose
  • lignin

Published Papers (4 papers)

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Research

18 pages, 5184 KiB  
Article
Lignocellulose Fermentation Products Generated by Giant Panda Gut Microbiomes Depend Ultimately on pH Rather than Portion of Bamboo: A Preliminary Study
by Alberto Scoma, Way Cern Khor, Marta Coma, Robert Heyer, Ruben Props, Tim Bouts, Dirk Benndorf, Desheng Li, Hemin Zhang and Korneel Rabaey
Microorganisms 2022, 10(5), 978; https://doi.org/10.3390/microorganisms10050978 - 07 May 2022
Viewed by 1916
Abstract
Giant pandas feed almost exclusively on bamboo but miss lignocellulose-degrading genes. Their gut microbiome may contribute to their nutrition; however, the limited access to pandas makes experimentation difficult. In vitro incubation of dung samples is used to infer gut microbiome activity. In pandas, [...] Read more.
Giant pandas feed almost exclusively on bamboo but miss lignocellulose-degrading genes. Their gut microbiome may contribute to their nutrition; however, the limited access to pandas makes experimentation difficult. In vitro incubation of dung samples is used to infer gut microbiome activity. In pandas, such tests indicated that green leaves are largely fermented to ethanol at neutral pH and yellow pith to lactate at acidic pH. Pandas may feed on either green leaves or yellow pith within the same day, and it is unclear how pH, dung sample, fermentation products and supplied bamboo relate to one another. Additionally, the gut microbiome contribution to solid bamboo digestion must be appropriately assessed. Here, gut microbiomes derived from dung samples with mixed colors were used to ferment green leaves, also by artificially adjusting the initial pH. Gut microbiomes digestion of solid lignocellulose accounted for 30–40% of the detected final fermentation products. At pH 6.5, mixed-color dung samples had the same fermentation profile as green dung samples (mainly alcohols), while adjusting the initial pH to 4.5 resulted in the profile of yellow dung samples (mainly lactate). Metaproteomics confirmed that gut microbiomes attacked hemicellulose, and that the panda’s alpha amylase was the predominant enzyme (up to 75%). Full article
(This article belongs to the Special Issue Lignocellulose Degradation by Gut Microbiomes, from Mammals to Insects)
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14 pages, 2588 KiB  
Article
Identification of a New Endo-β-1,4-xylanase Prospected from the Microbiota of the Termite Heterotermes tenuis
by Olinda S. A. Alcobaça, Emeline B. Campanini, Iara Ciancaglini, Sâmara V. Rocha, Iran Malavazi, Caio C. M. Freire, Francis M. F. Nunes, Andrea S. C. Fuentes and Anderson F. Cunha
Microorganisms 2022, 10(5), 906; https://doi.org/10.3390/microorganisms10050906 - 26 Apr 2022
Cited by 1 | Viewed by 1843
Abstract
Xylanases are hemicellulases that break down xylan to soluble pentoses. They are used for industrial purposes, such as paper whitening, beverage clarification, and biofuel production. The second-generation bioethanol production is hindered by the enzymatic hydrolysis step of the lignocellulosic biomass, due to the [...] Read more.
Xylanases are hemicellulases that break down xylan to soluble pentoses. They are used for industrial purposes, such as paper whitening, beverage clarification, and biofuel production. The second-generation bioethanol production is hindered by the enzymatic hydrolysis step of the lignocellulosic biomass, due to the complex arrangement established among its constituents. Xylanases can potentially increase the production yield by improving the action of the cellulolytic enzyme complex. We prospected endo-β-1,4-xylanases from meta-transcriptomes of the termite Heterotermes tenuis. In silico structural characterization and functional analysis of an endo-β-1,4-xylanase from a symbiotic protist of H. tenuis indicate two active sites and a substrate-binding groove needed for the catalytic activity. No N-glycosylation sites were found. This endo-β-1,4-xylanase was recombinantly expressed in Pichia pastoris and Escherichia coli cells, presenting a molecular mass of approximately 20 kDa. Enzymatic activity assay using recombinant endo-β-1,4-xylanase was also performed on 1% xylan agar stained with Congo red at 30 °C and 40 °C. The enzyme expressed in both systems was able to hydrolyze the substrate xylan, becoming a promising candidate for further analysis aiming to determine its potential for application in industrial xylan degradation processes. Full article
(This article belongs to the Special Issue Lignocellulose Degradation by Gut Microbiomes, from Mammals to Insects)
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23 pages, 20160 KiB  
Article
Enrichment of Anaerobic Microbial Communities from Midgut and Hindgut of Sun Beetle Larvae (Pachnoda marginata) on Wheat Straw: Effect of Inoculum Preparation
by Bruna Grosch Schroeder, Washington Logroño, Ulisses Nunes da Rocha, Hauke Harms and Marcell Nikolausz
Microorganisms 2022, 10(4), 761; https://doi.org/10.3390/microorganisms10040761 - 31 Mar 2022
Cited by 9 | Viewed by 2641
Abstract
The Pachnoda marginata larva have complex gut microbiota capable of the effective conversion of lignocellulosic biomass. Biotechnological utilization of these microorganisms in an engineered system can be achieved by establishing enrichment cultures using a lignocellulosic substrate. We established enrichment cultures from contents of [...] Read more.
The Pachnoda marginata larva have complex gut microbiota capable of the effective conversion of lignocellulosic biomass. Biotechnological utilization of these microorganisms in an engineered system can be achieved by establishing enrichment cultures using a lignocellulosic substrate. We established enrichment cultures from contents of the midgut and hindgut of the beetle larva using wheat straw in an alkaline medium at mesophilic conditions. Two different inoculation preparations were used: procedure 1 (P1) was performed in a sterile bench under oxic conditions using 0.4% inoculum and small gauge needles. Procedure 2 (P2) was carried out under anoxic conditions using more inoculum (4%) and bigger gauge needles. Higher methane production was achieved with P2, while the highest acetic acid concentrations were observed with P1. In the enrichment cultures, the most abundant bacterial families were Dysgonomonadaceae, Heliobacteriaceae, Ruminococcaceae, and Marinilabiliaceae. Further, the most abundant methanogenic genera were Methanobrevibacter, Methanoculleus, and Methanosarcina. Our observations suggest that in samples processed with P1, the volatile fatty acids were not completely converted to methane. This is supported by the finding that enrichment cultures obtained with P2 included acetoclastic methanogens, which might have prevented the accumulation of acetic acid. We conclude that differences in the inoculum preparation may have a major influence on the outcome of enrichment cultures from the P. marginata larvae gut. Full article
(This article belongs to the Special Issue Lignocellulose Degradation by Gut Microbiomes, from Mammals to Insects)
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24 pages, 5693 KiB  
Article
Valorization Potential of a Novel Bacterial Strain, Bacillus altitudinis RSP75, towards Lignocellulose Bioconversion: An Assessment of Symbiotic Bacteria from the Stored Grain Pest, Tribolium castaneum
by Mudasir A. Dar, Neeraja P. Dhole, Rongrong Xie, Kiran D. Pawar, Kalim Ullah, Praveen Rahi, Radhakrishna S. Pandit and Jianzhong Sun
Microorganisms 2021, 9(9), 1952; https://doi.org/10.3390/microorganisms9091952 - 14 Sep 2021
Cited by 30 | Viewed by 2964
Abstract
Bioconversion of lignocellulose into renewable energy and commodity products faces a major obstacle of inefficient saccharification due to its recalcitrant structure. In nature, lignocellulose is efficiently degraded by some insects, including termites and beetles, potentially due to the contribution from symbiotic gut bacteria. [...] Read more.
Bioconversion of lignocellulose into renewable energy and commodity products faces a major obstacle of inefficient saccharification due to its recalcitrant structure. In nature, lignocellulose is efficiently degraded by some insects, including termites and beetles, potentially due to the contribution from symbiotic gut bacteria. To this end, the presented investigation reports the isolation and characterization of cellulolytic bacteria from the gut system of red flour beetle, Tribolium castaneum. Out of the 15 isolated bacteria, strain RSP75 showed the highest cellulolytic activities by forming a clearance zone of 28 mm in diameter with a hydrolytic capacity of ~4.7. The MALDI-TOF biotyping and 16S rRNA gene sequencing revealed that the strain RSP75 belongs to Bacillus altitudinis. Among the tested enzymes, B. altitudinis RSP75 showed maximum activity of 63.2 IU/mL extract for xylanase followed by β-glucosidase (47.1 ± 3 IU/mL extract) which were manifold higher than previously reported activities. The highest substrate degradation was achieved with wheat husk and corn cob powder which accounted for 69.2% and 54.5%, respectively. The scanning electron microscopy showed adhesion of the bacterial cells with the substrate which was further substantiated by FTIR analysis that depicted the absence of the characteristic cellulose bands at wave numbers 1247, 1375, and 1735 cm−1 due to hydrolysis by the bacterium. Furthermore, B. altitudinis RSP75 showed co-culturing competence with Saccharomyces cerevisiae for bioethanol production from lignocellulose as revealed by GC-MS analysis. The overall observations signify the gut of T. castaneum as a unique and impressive reservoir to prospect for lignocellulose-degrading bacteria that can have many biotechnological applications, including biofuels and biorefinery. Full article
(This article belongs to the Special Issue Lignocellulose Degradation by Gut Microbiomes, from Mammals to Insects)
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