Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates

2022 ◽  
pp. gr.275533.121
Author(s):  
Tyler A Joseph ◽  
Philippe Chlenski ◽  
Aviya Litman ◽  
Tal Korem ◽  
Itsik Pe'er
Keyword(s):  
Growth Rates ◽  
Microbial Growth ◽  
Bacterial Genome ◽  
Growth Dynamics ◽  
Disease Status ◽  
Reference Database ◽  
Metagenomic Sequencing ◽  
Biological Interpretation ◽  
Relative Abundances ◽  
Host Microbe Interactions

Patterns of sequencing coverage along a bacterial genome---summarized by a peak-to-trough ratio (PTR)---have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce CoPTR (Compute PTR): a tool for computing PTRs from complete reference genomes and assemblies. Using simulations and data from growth experiments in simple and complex communities, we show that CoPTR is more accurate than the current state-of-the-art, while also providing more PTR estimates overall. We further develop theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with inflammatory bowel disease. We show that growth rates are personalized, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by demonstrating how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.

scholarly journals Accurate and robust inference of microbial growth dynamics from metagenomic sequencing

2021 ◽  
Author(s):  
Tyler A. Joseph ◽  
Philippe Chlenski ◽  
Tal Korem ◽  
Itsik Pe’er
Keyword(s):  
Microbial Growth ◽  
Bacterial Genome ◽  
Growth Dynamics ◽  
Disease Status ◽  
Reference Database ◽  
Metagenomic Sequencing ◽  
Link Type ◽  
Biological Interpretation ◽  
Relative Abundances ◽  
Host Microbe Interactions

AbstractPatterns of sequencing coverage along a bacterial genome—summarized by a peak-to-trough ratio (PTR)—have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce CoPTR (Compute PTR): a tool for computing PTRs from complete reference genomes and assemblies. We show that CoPTR is more accurate than the current state-of-the-art, while also providing more PTR estimates overall. We further develop theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with irritable bowel disease. We show that PTRs have high inter-individual variation, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by demonstrating how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.AvailabilityCoPTR is available from https://github.com/tyjo/coptr, with documentation on https://coptr.readthedocs.io.

GROWTH OF PIKE-PERCH SANDER LUCIOPERCA (L., 1758) (PERCIDAE) IN RESERVOIRS OF K. SATPAYEV’S CHANNEL

2018 ◽  
pp. 59-68
Author(s):  
Saule Zhangirovna Asylbekova ◽  
Kuanysh Baibulatovich Isbekov ◽  
Vladimir Nickolaevich Krainyuk
Keyword(s):  
Growth Rates ◽  
Growth Dynamics ◽  
High Growth ◽  
Water Bodies ◽  
Volga River ◽  
Trophic Resources ◽  
Pike Perch ◽  
The Amur River ◽  
Back Calculation ◽  
Abiotic And Biotic Factors

Pike-perch is an invader for the water basins of Central Kazakhstan. These species have stable self-reproductive populations in the regional waters. Back calculation method was used to investigate pike-perch growth rates in reservoirs of K. Satpayev’s channel. For comparison, the data from the other water bodies (Vyacheslavsky and Sherubay-Nurinsky water reservoirs) were used, as well as literature data. Pike-perch species from the investigated waters don’t show high growth rates. The populations from the reservoirs of K. Satpayev’s channel have quite similar growth rates with populations from the Amur river, from a number of reservoirs in the Volga river basin and from the reservoir in Spain. Sexual differences in growth have not been observed. Evaluating possible influence of various abiotic and biotic factors on the growth rate of pike-perch in the reservoirs of K. Satpayev’s channel was carried out. It has been stated that the availability of trophic resources cannot play a key role in growth dynamics because of their high abundance. Morphology of water bodies also does not play a role, as well as chromaticity, turbidity and other optical water indicators. It can be supposed that the main factor influencing growth of pike perch is the habitat’s temperature. This factor hardly ever approaches optimal values for the species in reservoirs of K. Satpaev’s channel. The possible influence of fishing selectivity on pike-perch growth rates was also evaluated. Currently, there has been imposed a moratorium on pike-perch catch. However, pike-perch is found in by-catches and in catches of amateur fishermen. It should be said that such seizures have an insignificant role in the dynamics of growth rates.

Microbial growth rates in nature.

1971 ◽  
Vol 35 (1) ◽  
pp. 39-58 ◽  
Author(s):  
T D Brock
Keyword(s):  
Growth Rates ◽  
Microbial Growth

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

Wintertime growth in Atlantic salmon under changing climate: the importance of ice cover for individual growth dynamics

2021 ◽  
Author(s):  
Laura Härkönen ◽  
Pauliina Louhi ◽  
Riina Huusko ◽  
Ari Huusko
Keyword(s):  
Climate Change ◽  
Atlantic Salmon ◽  
Growth Rates ◽  
Growth Dynamics ◽  
Ice Cover ◽  
Individual Growth ◽  
Late Winter ◽  
Dynamic Nature ◽  
Individual Level ◽  
Growth Variation

Understanding the dynamic nature of individual growth in stream-dwelling salmonids may help forecast consequences of climate change on northern fish populations. Here, we performed an experimental capture-mark-recapture study in Atlantic salmon to quantify factors influencing wintertime growth variation among juveniles under different scenarios for ice cover reduction. We applied multiple imputation to simulate missing size observations for unrecaptured fish, and to account for individual-level variation in growth rates. The salmon parr exhibited substantial body length shrinkage in early winter, suppressed growth through mid-winter, and increasing growth rates in late winter and particularly in spring. Unexpectedly, the presence of ice cover had no direct effects on wintertime growth. Instead, our results implied increasing energetic costs with reducing ice cover: individuals exposed to absent or shortened ice-covered period gained mass at a lowered rate in spring whereas the present, long ice-covered period was followed by rapid growth. This study emphasizes natural resilience of Atlantic salmon to wintertime environmental variation which may help the species to cope with the reductions in ice cover duration due to climate change.

scholarly journals Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

2020 ◽  
Author(s):  
Roland C Wilhelm ◽  
Charles Pepe-Ranney ◽  
Pamela Weisenhorn ◽  
Mary Lipton ◽  
Daniel H. Buckley
Keyword(s):  
Microbial Growth ◽  
Competitive Exclusion ◽  
Antibiotic Production ◽  
Growth Dynamics ◽  
Soil Disturbance ◽  
Gliding Motility ◽  
Cellulolytic Microorganisms ◽  
Trade Offs ◽  
Self Sufficiency ◽  
Attachment Structures

Abstract Many cellulolytic microorganisms degrade cellulose through extracellular processes that yield free intermediates which promote interactions with non-cellulolytic organisms. We hypothesize that these interactions determine the ecological and physiological traits that govern the fate of cellulosic carbon (C) in soil. We evaluated the genomic potential of soil microorganisms that access C from 13 C-labeled cellulose. We used metagenomic-SIP and metaproteomics to evaluate whether cellulolytic and non-cellulolytic microbes that access 13 C from cellulose encode traits indicative of metabolic dependency or competitive exclusion. The most highly 13 C-enriched taxa were cellulolytic Cellvibrio ( Gammaproteobacteria ) and Chaetomium ( Ascomycota ), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. These ruderal taxa were common indicators of soil disturbance in agroecosystems, such as tillage and fertilization. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria , demonstrating differences in dependency among cellulose degraders. Non-cellulolytic taxa that accessed 13 C from cellulose ( Planctomycetales , Verrucomicrobia and Vampirovibrionales ) were highly dependent, as indicated by patterns of auxotrophy and 13 C-labeling (i.e. partial labelling or labeling at later-stages). Major 13 C-labeled cellulolytic microbes ( e.g. Sorangium, Actinomycetales, Rhizobiales and Caulobacteraceae ) possessed adaptations for surface colonization ( e.g. gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposition. These results suggest that access to cellulose was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion. These trade-offs likely influence microbial growth dynamics on particulate organic carbon and reveal that the fate of carbon is governed by a complex economy within the microbial community.

Evaluating the impact of changes in human capital structure on Russia's economic growth dynamics

2021 ◽  
Vol 20 (2) ◽  
pp. 200-222
Author(s):  
Roman M. MEL'NIKOV ◽  
Valentina A. TESLENKO
Keyword(s):  
Higher Education ◽  
Economic Growth ◽  
Growth Rates ◽  
Fixed Effects ◽  
Growth Dynamics ◽  
High Tech ◽  
Fixed Effects Model ◽  
Long Term Effects ◽  
Academic Degree ◽  
The Impact

Subject. The article explores the impact of changes in the educational structure of the employed population on the dynamics of economic growth. Objectives. The purpose is to evaluate the impact of changes in the share of employed persons, having secondary vocational and higher education, and researchers with academic degree on the growth rates of the Russian economy. Methods. The study employs the regression analysis of panel data of Russian regions, the specification with a quadratic dependence of economic growth rates on the share of employed persons, having the higher education and secondary vocational education. A fixed-effects model is used to analyze the short-term effects, the sustainability of results, and long-term effects, using the pool models and random effects models. Results. The increase in the share of researchers with academic degree has a positive and significant effect on economic growth, but only if adequate R&D funding is provided. The increase in the share of employed persons with higher education up to thirty percent is accompanied by an increase in the growth rate of real GRP in the long run, however, further expansion of higher education has no positive effect on economic growth. Conclusions. A powerful form of personnel training for Russian high-tech companies is a special model of ‘industrial postgraduate training’, which involves the collaboration of universities with industrial partners.

scholarly journals Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor

Gut ◽  
2020 ◽  
Vol 69 (11) ◽  
pp. 1998-2007 ◽  
Author(s):  
Yun Kit Yeoh ◽  
Zigui Chen ◽  
Martin C S Wong ◽  
Mamie Hui ◽  
Jun Yu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Fusobacterium Nucleatum ◽  
Disease Status ◽  
Rural Populations ◽  
Microbial Genomes ◽  
Microbiome Composition ◽  
Chinese Populations ◽  
Southern Chinese ◽  
Relative Abundances ◽  
Reference Genomes

ObjectiveFusobacteria are not common nor relatively abundant in non-colorectal cancer (CRC) populations, however, we identified multiple Fusobacterium taxa nearly absent in western and rural populations to be comparatively more prevalent and relatively abundant in southern Chinese populations. We investigated whether these represented known or novel lineages in the Fusobacterium genus, and assessed their genomes for features implicated in development of cancer.MethodsPrevalence and relative abundances of fusobacterial species were calculated from 3157 CRC and non-CRC gut metagenomes representing 16 populations from various biogeographies. Microbial genomes were assembled and compared with existing reference genomes to assess novel fusobacterial diversity. Phylogenetic distribution of virulence genes implicated in CRC was investigated.ResultsIrrespective of CRC disease status, southern Chinese populations harboured increased prevalence (maximum 39% vs 7%) and relative abundances (average 0.4% vs 0.04% of gut community) of multiple recognised and novel fusobacterial taxa phylogenetically distinct from Fusobacterium nucleatum. Genomes assembled from southern Chinese gut metagenomes increased existing fusobacterial diversity by 14.3%. Homologues of the FadA adhesin linked to CRC were consistently detected in several monophyletic lineages sister to and inclusive of F. varium and F. ulcerans, but not F. mortiferum. We also detected increased prevalence and relative abundances of F. varium in CRC compared with non-CRC cohorts, which together with distribution of FadA homologues supports a possible association with gut disease.ConclusionThe proportion of fusobacteria in guts of southern Chinese populations are higher compared with several western and rural populations in line with the notion of environment/biogeography driving human gut microbiome composition. Several non-nucleatum taxa possess FadA homologues and were enriched in CRC cohorts; whether this imposes a risk in developing CRC and other gut diseases deserves further investigation.

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