Abhijeet Singh

Uppsala University (UU) & Swedish University of Agricultural Sciences (SLU) · Department of Earth Sciences (UU) & Department of Molecular Sciences (SLU)

Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and acetate, during anaerobic digestion of protein-rich waste material. Studying the syntrophic communities that perform acid conversion is challenging, due to their relatively low abund...

Climate change has been intensifying soil drying and rewetting cycles, which can alter the soil microbiome structure and activity. Here we hypothesized that a soil drying-rewetting cycle enhances biodegradation and, hence, decreases the effectiveness of nitrification inhibitors (NIs). The effectiveness of DMPP (3,4-Dimethylpyrazole phosphate) and M...

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms an...

The objective was to determine the effects on rumen microbiome and milk quality of reducing the methane (CH4) produced from enteric fermentation by the addition of Asparagopsis taxiformis (AT) to the diets of dairy cows. Six Nordic Red cows at 122 ± 13.7 (mean ± SD) days in milk, of parity 2.7 ± 0.52 and producing 36 kg ± 2.5 kg milk per day at the...

Cattle manure has a low energy content and high fibre and water content, limiting its value for biogas production. Co‐digestion with a more energy‐dense material can improve the output, but the co‐substrate composition that gives the best results in terms of degree of degradation, gas production and digestate quality has not yet been identified. Th...

AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was al...

Cleans invalid bases/residues in DNA sequence file i.e., replaces invalid bases with Ns and optionally removes special characters from headers

PROTEINcleaner: a python utility to clean PROTEIN sequences and headers

SubsetSeq: a python utility to subset multisequence file based on identifiers from external text file

Lava tubes on Mars hold exciting potential for the preservation of biosignatures, which may survive on geological timescales in these isolated, stable environments. To support the development of future astrobiological mission concepts, we turn to terrestrial lava tubes, host to a variety of microbial communities and secondary minerals. Following a...

The manuscript was about microbial fermentation technology and recent advances

An anaerobic bacterial strain, designated AMB_01T, recovered from mesophilic propionate enrichment of a high-ammonia biogas digester, was characterised using phenotypic and molecular taxonomic methods. Cells of AMB_01T are coccus-shaped and often occur arranged as diplococci or sarcina. Growth occurred at 20-45 °C, initial pH 5.5-8.5 and with up to...

The manuscript was about in silico simulation analysis.

The manuscript was about cultivation in green houses.

Restriction fragment length polymorphism (RFLP) is a technology for the molecular characterization of DNA and widely used genome mapping, medical genetics, molecular microbiology and forensics etc. Terminal restriction fragment length polymorphism (T-RFLP), a variant of RFLP is extensively used in environmental microbiology for the microbial commun...

The manuscript was about analysis of salt-affected soils.

The manuscript was about composting of organic biomass.

AcetoBase is a public repository and database published in 2019, for the formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial formyltetrahydrofolate nucleotide and protein sequences from the genomes and metagenome assembled genomes (MAGs), as well as sequences generated by clone library sequencing....

Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection...

Sustainability, International Journal of Environmental Research and Public Health

Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gen...

Reviewer certificate

FilterByLength: Filter fasta sequences by length and count the sequences in a multifasta file

Biogas process has great potential for reducing the current dependence on fossil fuels and for climate mitigation and sustainable development. In this process organic matter is decomposed under anaerobic conditions by microorganisms to form biogas and a nutrient rich biofertiliser. For adequate use of the resources invested in commercial biogas pro...

Test dataset for AcetoScan

Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gen...

Our high-throughput FTHFS gene AmpSeq method for barcoded samples and unsupervised analysis with AcetoScan accurately reveals temporal dynamics of acetogenic community structure in anaerobic digesters.

Our high-throughput FTHFS gene AmpSeq method for barcoded samples and unsupervised analysis with AcetoScan accurately reveals temporal dynamics of acetogenic community structure in anaerobic digesters.

Inefficient syntrophic propionate degradation causes severe operating disturbances and reduces biogas productivity in many high‐ammonia anaerobic digesters, but propionate‐degrading microorganisms in these systems remain unknown. Here, we identified candidate ammonia‐tolerant syntrophic propionate‐oxidising bacteria using propionate enrichment at h...

User-manual for AcetoScan

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visuali...

CharReplace: a multipurpose program to replace special characters in file/directories names or rename files/directories

Gut dysbiosis has been implicated in the pathophysiology of a growing number of non-communicable diseases. High through-put sequencing technologies and short chain fatty acid (SCFA) profiling enables surveying of the composition and function of the gut microbiota and provide key insights into host-microbiome interactions. However, a methodological...

Genomic DNA extraction from anaerobic digester samples

DupRemover finds duplicate sequences and keeps unique sequence while concatenating all the fasta headers together in a nucleotide or amino acid multi-fasta file. ------ Code repository - https://github.com/abhijeetsingh1704/DupRemover

Gut dysbiosis has been implicated in the pathophysiology of a growing number of non-communicable diseases. High through-put sequencing technologies and short chain fatty acid (SCFA) profiling enables surveying of the composition and function of the gut microbiota and provide key insights into host-microbiome interactions. However, a methodological...

The Planetary Analogues and Exobiology Lava Tube Expedition (PELE) team investigates volcanic caves as Martian analogue sites. Here we present data from Icelandic lava tubes, with the aim of identifying biotically-formed speleothems as biosignatures.

Citation details: Singh,A., Müller,B., Fuxelius,HH. et al. AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences. Abstract Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impe...

A simple and convenient program to convert fasta sequences to fastq sequences, in casava 1.8 header format version.

The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (blaKPC) has been spreading over...

This programs calculates the approximate energy (ATP) required to form a peptide chain

Program to clean AMINO ACID fasta sequences and removes and illegal characters in sequence or any non-natural amino acid residue

Program to clean DNA fasta sequences and removes and illegal characters in sequence or any non-natural residue

this program takes multifasta file as input and gives a concatenated sequence as output

This bash code translates the binary data to DNA sequence

This is a bash program to translate DNA sequence (fasta format) to binary fasta format

Off-world lava caves sampling

The enrichment of CO2-reducing microbial biocathodes is challenging. Previous research has shown that a promising approach could be to first enrich bioanodes and then lower the potential so the electrodes are converted into biocathodes. However, the effect of such a transition on the microbial community on the electrode has not been studied. The go...

Lava tubes on Earth represent some of the most enticing Martian analog environments when investigating the possibility of past or present life on Mars. Lava tubes provide stable, sheltered environments which are isolated and protected from the radiation on the surface. The microbial mats in these caves further regulate the environment for life, all...

To enrich syntrophic acetate-oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)-dominated systems and continuously supplied with acetate (0.4 or 7.5 g l⁻¹) at high-ammonia levels. The chemostats were operated under mesophilic (37°C) or thermophilic (52°C) temperature for about six hyd...

Fig. S1. Acetate concentration in the high‐acetate chemostats (fed medium containing 7.5 g acetate l−1) operating at 37°C (A) and 52°C (B). Fig. S2. Rarefaction curves generated from OTUs at 3% sequence dissimilarity occuring in the four mesophilic and the four thermophilic chemostats operated in the present study. Fig. S3. Average richness (numb...

Phase contrast microscopy cannot give sufficient information on bacterial metabolic activity, or if a cell is dead, it has the fate to die or it is in a viable but non-growing state. Thus, a reliable sensing of the metabolic activity helps to distinguish different categories of viability. We present a non-invasive instantaneous sensing method using...

The susceptibility of bacteria to antibiotics is of immense interest for patients, physicians, pharmacol-ogists, and researchers due to the impact on global human health care of antibiotic tolerant or resistant bacteria (WHO, 2014). We introduce the use of a disposable inexpensive PDMS-glass biochip for spatial temporal resolved antibiotic sensitiv...

The antibiotic susceptibility of bacteria is an important criterion, as it has high relevance in the clinical treatment of infectious bacterial diseases and pharmacological research for new antimicrobial drug development. Antibiotic susceptibility testing is widely used for the analysis of bacterial sensitivity for an antibiotic. There is an increa...